This version focuses on improving the UX of JIPipe and introduces a new 3D scene creation feature.

User interface improvements

Drag to create slots

It is now possible to drag edges to an + add input slot button. After doing this, the user is prompted with an auto-configured “Add slot” dialog that comes with a pre-selected data type.

Redesigned external and adaptive parameters

We noticed that the “Advanced parameters” tab where parameter slots (external parameters) and adaptive parameters are configured confused many users. The tab was replaced with notification panels that are shown above the list of parameters.

Adaptive parameters are now shown inline, but can still be manually configured via the Configure menu.

Locking node size/position

It is now possible to lock the size and position of nodes via a parameter or by via the context menu / multi-selection panel.

Locked nodes can be selected and their parameters can be edited. But the user interface will ignore all user inputs regarding the movement and sizing (only graph annotations) of nodes.

The keybinding is L for locking the selected nodes and Ctrl+L for unlocking the selected nodes.

Moving nodes via arrow keys

It is now possible to use the arrow keys on your keyboard to move nodes around.

Locked nodes are not affected by this key bind.

Displaying the current tool next to the cursor

JIPipe will now display the name and icon of the current graph editor tool next to the cursor. The feature can be deactivated and configured in the JIPipe application settings.

Improved run dialog

Users reported that the “Run now” button was hard to see. It was moved into a large message panel at the top of the settings.

Button to switch to compartments editor

If users accidentally close the “Compartments” tab, it could only be re-opened by finding an entry in the Project menu. A button was added to switch to / reopen the compartments editor.

New update on parameter changes

The old “Auto update” functionality required that the whole pipeline was loaded and had many bugs. It was replaced by a new setting “Update on parameter changes” that can be found in any cache viewer.

Graph annotations

In older JIPipe versions, there was only one mode of annotating important parts of a pipeline via “Comment” nodes. This version introduces freely re-sizable annotation nodes that can be drawn by selecting the appropriate graph annotation tool in the left-hand graph tool bar. All operations in the graph tool bar now have a key bind.

Graph annotations are always displayed below functional nodes to ensure that no potentially important information is overlooked.

Filaments and ROI

2D ROI pairwise statistics

The “Extract pairwise 3D ROI statistics” node was backported to 2D.

Filaments display

The 3D Filaments data type now has a custom display operation. Filaments can be managed in the “Filaments” tab of the image viewer.

Images

Nodes for custom thresholds with min/max

The existing custom expression-based thresholding nodes only supported a max threshold. New nodes that support min and max thresholding were added.

Merging nodes

New nodes that allow merging of hyperstacks were added. Existing nodes were renamed.

Tables

Improved “Rename table column”

The node “Rename table column” was redesigned and the old version was deprecated. The new version allows to use expression for generating the new column names.

3D scenes generation and export

JIPipe can now generate static 3D scenes from masks, filaments, and 3D ROI. Scenes can be combined and exported into the Collada (*.dae) format.

Expressions

Alternative element access operator

Expressions now support the X[Y] operator additional to X@Y and X AT Y

Additional improvements

• JIPipe does not come anymore with a pre-packaged OMERO. Instead, the user can install any OMERO version they like. JIPipe will check if a valid OMERO installation is found.
• Trackmate: fixed bug where images with physical pixel sizes were not correctly handled
• Guava EventBus is replaced by a custom Observer event system. This resolved many memory-related issues (e.g., JIPipe filled all memory in a few hours even if the GUI is left alone)
• The icons for compartments were reworked
• Fixed rendering of shadows
• Faster node rendering by using a buffer
• Fix crop 2D not copying scale
• Fix expression @ / AT operator precedence
• Fix measuring 2D ROI not adding the name of ROI if no reference image is provided
• Fix TrackMate display not working with setting slices
• Fix 3D viewer LUT issues
• Improved CLI: –save-to-disk on/off and –output-results all/none/only-compartment-outputs were added