Download JIPipe 5.2.0
Latest version
The version was pushed to 5.2.0 due to the introduction of new features.
Upgrade notes
- Various ImageJ nodes: LUTs are now preserved due to changes in how LUTs are handled. This should not affect the analysis.
- Outline ROI: gained additional parameter for error handling. Defaults to throwing an error.
- Nodes that only input the OME XML from OME images have been changed so that they instead consume the OME XML. This does not affect the workflow due to an auto-conversion.
Additional image and ROI processing nodes
- Kuwahara filter (regular and linear variant in one node)
- Transform 2D ROI (all-in-one scale/translate/rotate)
- ROI outline node gained additional outlines: fit circle, fit spline, fit ellipse, remove spline fit, line to area, area to line
- Interpolate 2D ROI (converts all ROI into sub-pixel resolution ones)
- Box filter 2D (selectable radius)
- New nodes for inverting images that are clearer to understand
- Custom extended depth of focus (Z/C/T) that applies EDoF (just like the CLIJ function), but on GPU and with custom scoring input (optional)
- Annotate data with OME image metadata (allows to annotate any data with OME XML metadata)
- New data type: OME XML (can be converted from XML and from an OME Image)
- Read OME XML from file (reads only the OME XML from an image)
- Merge channels (composite): similar to Merge channels (classic), but always creates a composite and allows the setup of custom LUT colors
OMERO interactive login
In previous JIPipe versions, the full OMERO credentials had to be provided in the node, project, or application. The credentials now can be left out, which will trigger a login dialog when the pipeline is executed. After the pipeline run, the credentials are then automatically cleared from memory.
Enhancements
- Add nodes panel: now also contains dedicated entries for aliases
- Dock component: you can now keep dock panels open even if no content is shown by right-clicking the sidebar and selecting Always show panel
- Path editor now has an easy-to-understand “Select” button
- Some common variants/parameters of algorithms have now dedicated example entries in the node database (e.g., Otsu thresholding)
- Z-Project now preserves LUTs unless it’s configured to channel-project
- Renamed Merge channels into Merge channels (classic)
Bugfixes
- Focusing issue with search bar was resolved
- Windows: drive letters not shown in file manager
- File chooser: go to home directory if directory is invalid
- Unable to create parameter sets from within groups
- Project overview was not listing referenced parameters
- Histogram in image viewer was wrong for 32-bit and 16-bit images
- Fast image arithmetics: examples were not instantiated properly
Known issues
- JIPipe currently has no secure way to pass OMERO credentials via CLI