A set of basic written tutorials that were initially released in 2022. Please note that while the basic principles behind JIPipe remain the same, the user interface has significantly changed over years of development.

We decided to remove some tutorials compared to the old website that are not even closely up-to-date anymore.

Basic tutorials (2022) - Adding and running nodes

Explains how to add new nodes into a project and use them to load an image file. Afterwards, the project is saved.

Basic tutorials (2022) - Importing images

A short step-by-step guide that explains how to import an image

Basic tutorials (2022) - Changing node parameters

A short tutorial that explains how to change node parameters.

Basic tutorials (2022) - Importing a directory of images (1/2)

A tutorial that explains how to import multiple images from a directory

Basic tutorials (2022) - Importing a directory of images (2/2)

Continuation of the previous tutorial about how to import a directory of images

Basic tutorials (2022) - Handling multi-channel images

A step-by-step tutorial that explains how to process multi-channel images by splitting the channels

Basic tutorials (2022) - Annotation-based filtering

A step-by-step guide that explains how to annotate images and filter them by annotations

Basic tutorials (2022) - Annotation-based branching

Continuation of the last tutorial that explains how to apply conditional data processing through branching

Basic tutorials (2022) - Modifying and merging annotations

Explains how to control annotations through modification and merging operations

Basic tutorials (2022) - Creating and connecting compartments

A step-by-step tutorial that explains how to organize projects into compartments for enhanced readability

Basic tutorials (2022) - Basic image segmentation with compartments

Continuation of the previous tutorial that showcases how to implement a basic image analysis pipeline that uses compartments for workflow organization

Basic tutorials (2022) - Quantification and plotting

Explains how to extract basic quantification results and plot them

Basic tutorials (2022) - Working with physical pixel sizes

Short guide that explains how to store physical pixel sizes into the set of annotations

Basic tutorials (2022) - ROI processing and visualization

Step-by-step guide that explains how to filter ROIs, use them for extracting statistics, and create visualizations

Basic tutorials (2022) - Table processing

A short tutorial on how to process tables by adding columns and creating summaries

Basic tutorials (2022) - Annotating data with measurements

A short tutorial that explains how to attach measurements to data