Data types

2D FFT Image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains two image files: fht.ome.tif / fht.tif and power_spectrum.ome.tif / power_spectrum.tif, as well as a file fht_info.json. Either the OME TIFF or TIFF must be present. fht.ome.tif / fht.tif contains the FHT (float32). power_spectrum.ome.tif / power_spectrum.tif contains the power spectrum (float32). fht_info.json contains a JSON object that defines following properties: quadrant-swap-needed (boolean), original-width (integer), original-height (integer), original-bit-depth (integer; 8, 16, or 32 are valid values), power-spectrum-mean (double).

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json

Developer information

Data type IDimagej-imgplus-fft-2d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D Image (Color)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-color
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (16 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-greyscale-16u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (8 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-greyscale-8u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (HSB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-color-hsb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (LAB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-color-lab
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (RGB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-color-rgb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (float)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-greyscale-32f
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (greyscale)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-greyscale
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D image (mask)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-2d-greyscale-mask
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

2D pie plot

Plot that shows the amount for each category as slice in a pie.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-pie-2d
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

3D FFT Image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains two image files: fht.ome.tif / fht.tif and power_spectrum.ome.tif / power_spectrum.tif, as well as a file fht_info.json. Either the OME TIFF or TIFF must be present. fht.ome.tif / fht.tif contains the FHT (float32). power_spectrum.ome.tif / power_spectrum.tif contains the power spectrum (float32). fht_info.json contains a JSON object that defines following properties: quadrant-swap-needed (boolean), original-width (integer), original-height (integer), original-bit-depth (integer; 8, 16, or 32 are valid values), power-spectrum-mean (double).

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json

Developer information

Data type IDimagej-imgplus-fft-3d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D Image (Color)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-color
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (16 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-greyscale-16u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (8 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-greyscale-8u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (HSB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-color-hsb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (LAB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-color-lab
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (RGB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-color-rgb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (float)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-greyscale-32f
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (greyscale)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-greyscale
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D image (mask)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-3d-greyscale-mask
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

3D pie plot

Plot that shows the amount for each category as slice in a pie.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-pie-3d
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

4D FFT Image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains two image files: fht.ome.tif / fht.tif and power_spectrum.ome.tif / power_spectrum.tif, as well as a file fht_info.json. Either the OME TIFF or TIFF must be present. fht.ome.tif / fht.tif contains the FHT (float32). power_spectrum.ome.tif / power_spectrum.tif contains the power spectrum (float32). fht_info.json contains a JSON object that defines following properties: quadrant-swap-needed (boolean), original-width (integer), original-height (integer), original-bit-depth (integer; 8, 16, or 32 are valid values), power-spectrum-mean (double).

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json

Developer information

Data type IDimagej-imgplus-fft-4d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D Image (Color)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-color
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (16 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-greyscale-16u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (8 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-greyscale-8u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (HSB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-color-hsb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (LAB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-color-lab
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (RGB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-color-rgb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (float)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-greyscale-32f
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (greyscale)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-greyscale
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

4D image (mask)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-4d-greyscale-mask
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D FFT Image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains two image files: fht.ome.tif / fht.tif and power_spectrum.ome.tif / power_spectrum.tif, as well as a file fht_info.json. Either the OME TIFF or TIFF must be present. fht.ome.tif / fht.tif contains the FHT (float32). power_spectrum.ome.tif / power_spectrum.tif contains the power spectrum (float32). fht_info.json contains a JSON object that defines following properties: quadrant-swap-needed (boolean), original-width (integer), original-height (integer), original-bit-depth (integer; 8, 16, or 32 are valid values), power-spectrum-mean (double).

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json

Developer information

Data type IDimagej-imgplus-fft-5d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D Image (Color)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-color
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (16 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-greyscale-16u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (8 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-greyscale-8u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (HSB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-color-hsb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (LAB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-color-lab
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (RGB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-color-rgb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (float)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-greyscale-32f
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (greyscale)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-greyscale
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

5D image (mask)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-5d-greyscale-mask
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Annotation table

A table that contains data annotations and other metadata

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.csv file that contains the table data.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/results-table.schema.json

Developer information

Data type IDannotation-table
Storage schema URLhttps://jipipe.org/schemas/datatypes/results-table.schema.json
Plugin nameAnnotation data types and algorithms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Bar category plot

Bar chart that displays categories in its X axis and colors the bars according to the group.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-category-bar
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Boolean input form

A form element that allows the user to input a boolean (true/false) value

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDboolean-form
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Box plot

Box and whisker plot.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-box-and-whisker
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Cellpose model

A Cellpose model

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

A single file without extension that contains the Cellpose model

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/cellpose-model-data.schema.json

Developer information

Data type IDcellpose-model
Storage schema URLhttps://jipipe.org/schemas/datatypes/cellpose-model-data.schema.json
Plugin nameCellpose integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationStringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature Methods, 18(1), 100-106.

Cellpose size model

A Cellpose size model

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

A single .npy file that contains the Cellpose size model

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/cellpose-size-model-data.schema.json

Developer information

Data type IDcellpose-size-model
Storage schema URLhttps://jipipe.org/schemas/datatypes/cellpose-size-model-data.schema.json
Plugin nameCellpose integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationStringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature Methods, 18(1), 100-106.

Data

Generic data

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Unknown storage schema (generic data)

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json

Developer information

Data type IDjipipe:data
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json
Plugin nameCore
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012), "Fiji: an open-source platform for biological-image analysis", Nature methods 9(7): 676-682, PMID 22743772, doi:10.1038/nmeth.2019
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationRueden, C., Schindelin, J., Hiner, M. & Eliceiri, K. (2016). SciJava Common [Software]. https://scijava.org/.

Data table

A table of data

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Stores a data table in the standard JIPipe format (data-table.json plus numeric slot folders)

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-data-table.schema.json

Developer information

Data type IDjipipe:data-table
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-data-table.schema.json
Plugin nameCore
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012), "Fiji: an open-source platform for biological-image analysis", Nature methods 9(7): 676-682, PMID 22743772, doi:10.1038/nmeth.2019
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationRueden, C., Schindelin, J., Hiner, M. & Eliceiri, K. (2016). SciJava Common [Software]. https://scijava.org/.

Empty data

An empty data type

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The storage folder is empty.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json

Developer information

Data type IDjipipe:empty-data
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json
Plugin nameCore
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012), "Fiji: an open-source platform for biological-image analysis", Nature methods 9(7): 676-682, PMID 22743772, doi:10.1038/nmeth.2019
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationRueden, C., Schindelin, J., Hiner, M. & Eliceiri, K. (2016). SciJava Common [Software]. https://scijava.org/.

FFT Image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains two image files: fht.ome.tif / fht.tif and power_spectrum.ome.tif / power_spectrum.tif, as well as a file fht_info.json. Either the OME TIFF or TIFF must be present. fht.ome.tif / fht.tif contains the FHT (float32). power_spectrum.ome.tif / power_spectrum.tif contains the power spectrum (float32). fht_info.json contains a JSON object that defines following properties: quadrant-swap-needed (boolean), original-width (integer), original-height (integer), original-bit-depth (integer; 8, 16, or 32 are valid values), power-spectrum-mean (double).

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json

Developer information

Data type IDimagej-imgplus-fft
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-fft-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

File

A path to a file

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file. The JSON data has following structure:

{
“jipipe:data-type”: “[Data type ID]”,
“path”: “[The path]”
}

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/path-data.schema.json

Developer information

Data type IDfile
Storage schema URLhttps://jipipe.org/schemas/datatypes/path-data.schema.json
Plugin nameFilesystem types and algorithms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Folder

A path to a directory

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file. The JSON data has following structure:

{
“jipipe:data-type”: “[Data type ID]”,
“path”: “[The path]”
}

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/path-data.schema.json

Developer information

Data type IDfolder
Storage schema URLhttps://jipipe.org/schemas/datatypes/path-data.schema.json
Plugin nameFilesystem types and algorithms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Form

Data that describes a user input element.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDform
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

GPU image

Image data stored on the GPU utilized by CLIJ

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpeg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDclij2-image
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameCLIJ2 integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRobert Haase, Loic Alain Royer, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, Eugene W Myers. CLIJ: GPU-accelerated image processing for everyone. Nat Methods 17, 5-6 (2020)

Group header form

Generates a group header element that allows to structure forms.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDgroup-header-form
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Histogram plot

Bar chart that displays the number of items for each bin. Please note that this plot requires raw values as input. A pre-defined histogram table should be rendered with an XY bar plot.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-histogram
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Image

An ImageJ image

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (16 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-greyscale-16u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (8 bit)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-greyscale-8u
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (Color)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-color
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (HSB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-color-hsb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (LAB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-color-lab
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (RGB)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-color-rgb
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (float)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-greyscale-32f
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (greyscale)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-greyscale
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Image (mask)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one image file with one of following extensions: *.tif, *.tiff, *.png, *.jpeg, *.jpg, *.png. We recommend the usage of TIFF.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/imageplus-data.schema.json

Developer information

Data type IDimagej-imgplus-greyscale-mask
Storage schema URLhttps://jipipe.org/schemas/datatypes/imageplus-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Integer input form

A form element that allows the user to input an integer number

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDinteger-form
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

JIPipe output

Output of a JIPipe run

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file. The JSON data has following structure:

{
“jipipe:data-type”: “[Data type ID]”,
“path”: “[The path]”
}

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/path-data.schema.json

Developer information

Data type IDjipipe-run-output
Storage schema URLhttps://jipipe.org/schemas/datatypes/path-data.schema.json
Plugin nameUtilities
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Json

Text in JSON format

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file that stores the current data.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-json-data.schema.json

Developer information

Data type IDjson
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-json-data.schema.json
Plugin nameStrings
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

LUT

A function that converts an intensity to a RGB color value

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one file in *.json format that describes the LUT gradient stops.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/lut-data.schema.json

Developer information

Data type IDimagej-lut
Storage schema URLhttps://jipipe.org/schemas/datatypes/lut-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Line category plot

Line chart that displays categories in its X axis and colors the lines according to the group.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-category-line
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Number input form

A form element that allows the user to input a real number

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDnumber-form
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Numeric table column

A table column that contains numbers (64bit floating point)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.csv file that contains the table data.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/results-table.schema.json

Developer information

Data type IDtable-column-numeric
Storage schema URLhttps://jipipe.org/schemas/datatypes/results-table.schema.json
Plugin nameStandard table operations
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675

OME Image

Image that contains additional OME-XML metadata. It can be converted into an image, a ROI list, or an XML text.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one or multiple files in *.tif or *.ome.tif format. If OME TIFF is used, multiple tiff files can be present (due to the ability of OME TIFF to link them together). Although, we do recommend having multiple files, as sometimes OME TIFF can store absolute paths. If only standard TIFF files are present, only one will be loaded.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/ome-image-data.schema.json

Developer information

Data type IDimagej-ome
Storage schema URLhttps://jipipe.org/schemas/datatypes/ome-image-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

OMERO Dataset

An OMERO dataset ID

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file that stores the

dataset-id
in a JSON object.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/omero-dataset-reference-data.schema.json

Developer information

Data type IDomero-dataset-id
Storage schema URLhttps://jipipe.org/schemas/datatypes/omero-dataset-reference-data.schema.json
Plugin nameOMERO Integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

OMERO Group

An OMERO group ID

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file that stores the

group-id
in a JSON object.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/omero-group-data.schema.json

Developer information

Data type IDomero-group-id
Storage schema URLhttps://jipipe.org/schemas/datatypes/omero-group-data.schema.json
Plugin nameOMERO Integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

OMERO Image

An OMERO image ID

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file that stores the

image-id
in a JSON object.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/omero-image-reference-data.schema.json

Developer information

Data type IDomero-image-id
Storage schema URLhttps://jipipe.org/schemas/datatypes/omero-image-reference-data.schema.json
Plugin nameOMERO Integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

OMERO Project

An OMERO project ID

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file that stores the

project-id
in a JSON object.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/omero-project-reference-data.schema.json

Developer information

Data type IDomero-project-id
Storage schema URLhttps://jipipe.org/schemas/datatypes/omero-project-reference-data.schema.json
Plugin nameOMERO Integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Output data

Output of a compartment

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

This is a structural data type. The storage folder is empty.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json

Developer information

Data type IDjipipe:compartment-output
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json
Plugin nameCompartment management
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Parameters

Contains algorithm parameters

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file that stores the parameters. The JSON data is an object with keys being the parameter keys. The value is an object with two items value and type-id. value contains the serialized parameter value. type-id contains the standardized parameter type ID.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/parameters-data.schema.json

Developer information

Data type IDparameters
Storage schema URLhttps://jipipe.org/schemas/datatypes/parameters-data.schema.json
Plugin nameMulti parameters data types
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Path

A file or folder

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.json file. The JSON data has following structure:

{
“jipipe:data-type”: “[Data type ID]”,
“path”: “[The path]”
}

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/path-data.schema.json

Developer information

Data type IDpath
Storage schema URLhttps://jipipe.org/schemas/datatypes/path-data.schema.json
Plugin nameFilesystem types and algorithms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Path input form

A form element that allows the user to input a path to a file or folder

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDpath-form
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Plot

A plot

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

ROI list

Collection of ROI

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains one file in *.roi or *.zip format. *.roi is a single ImageJ ROI. *.zip contains multiple ImageJ ROI. Please note that if multiple .roi/.zip are present, only one will be loaded.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/roi-list-data.schema.json

Developer information

Data type IDimagej-roi
Storage schema URLhttps://jipipe.org/schemas/datatypes/roi-list-data.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Results table

An ImageJ table

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.csv file that contains the table data.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/results-table.schema.json

Developer information

Data type IDimagej-results-table
Storage schema URLhttps://jipipe.org/schemas/datatypes/results-table.schema.json
Plugin nameImageJ integration
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675
Additional citationMelissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782

Row index table column

A table column that generates each row based on the current row index

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

This is a structural data type. The storage folder is empty.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json

Developer information

Data type IDtable-column-row-index
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json
Plugin nameStandard table operations
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675

Selection input form

A form element that allows the user to select one of multiple options

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDenum-form
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Stacked bar category plot

Bar chart that displays categories in its X axis and colors the bars according to the group. Bars within the same group are stacked.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-category-bar-stacked
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Statistical bar category plot

Bar chart that displays categories in its X axis and colors the bars according to the group. The bar height is the mean of each condition’s values. Shows an error bar.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-category-statistical-bar
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Statistical line category plot

Line chart that displays categories in its X axis and colors the lines according to the group. The line Y value is the mean of each condition’s values. Shows an error bar.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-category-statistical-line
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

String

A text

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.txt file that stores the current string.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/string-data.schema.json

Developer information

Data type IDstring
Storage schema URLhttps://jipipe.org/schemas/datatypes/string-data.schema.json
Plugin nameStrings
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

String table column

A table column that contains text values

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.csv file that contains the table data.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/results-table.schema.json

Developer information

Data type IDtable-column-string
Storage schema URLhttps://jipipe.org/schemas/datatypes/results-table.schema.json
Plugin nameStandard table operations
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675

Table column

A table column

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

This is a generic data type. The storage folder is empty.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json

Developer information

Data type IDtable-column
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json
Plugin nameStandard table operations
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675

Text input form

A form element that allows the user to input text

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a file forms.json that stores all metadata of the current form type in JSON format.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/form-data.schema.json

Developer information

Data type IDstring-form
Storage schema URLhttps://jipipe.org/schemas/datatypes/form-data.schema.json
Plugin nameForms
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

XML

Text in extended markup language (XML)

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

Contains a single *.xml file that stores the current data.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/xml-data.schema.json

Developer information

Data type IDxml
Storage schema URLhttps://jipipe.org/schemas/datatypes/xml-data.schema.json
Plugin nameStrings
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

XY line plot

Plot that displays the Y values against the X values.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-xy-line
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

XY scatter plot

Plot that displays the Y values against the X values.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

The folder contains following files:



The plot metadata JSON contains entries title, export-width,export-height, background-color, grid-color, with-legend, title-font-size, legend-font-size, color-map, and plot-series.
plot-series is mandatory and is a list of objects with each object having an object metadata, and a string element file-name. The file name must point at the corresponding series[Index].csv file of the series. Additional metadata in the root object and series metadata depend on the exact plot type.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/plot-data.schema.json

Developer information

Data type IDplot-xy-scatter
Storage schema URLhttps://jipipe.org/schemas/datatypes/plot-data.schema.json
Plugin nameStandard plots
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause

Zero table column

A table column that generates zeros for each row.

Trivial conversions

A trivial conversion involves no potentially expensive conversion operation. The data will directly match to input slots of the converted type. The edge has a dark-gray color.

This type can be trivially converted into following types:

This type can be trivially converted from following types:

Non-trivial conversions

A non-trivial conversion is defined by the developer and might involve some more complex conversion operations. They are indicated as blue edge.

This type can be also converted into following types:

This type can be also converted from following types:

Data storage

Following information was provided about the standardized storage of this data type:

This is a structural data type. The storage folder is empty.

Please visit following link for a JSON schema that describes the data storage: https://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json

Developer information

Data type IDtable-column-zero
Storage schema URLhttps://jipipe.org/schemas/datatypes/jipipe-empty-data.schema.json
Plugin nameStandard table operations
Plugin authorZoltán Cseresnyés*
Plugin authorRuman Gerst*
Plugin authorMarc Thilo Figge#
Plugin websitehttps://www.jipipe.org/
Plugin citation
Plugin licenseBSD 2-Clause
Additional citationRueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), "ImageJ2: ImageJ for the next generation of scientific image data", BMC Bioinformatics 18:529
Additional citationSchneider, C. A.; Rasband, W. S. & Eliceiri, K. W. (2012), "NIH Image to ImageJ: 25 years of image analysis", Nature methods 9(7): 671-675