Version 1.74.0

Plugin manager

In older JIPipe versions, all extensions are automatically loaded during the JIPipe startup. This was changed to reduce the number of dependencies by letting the users decide which extensions should be loaded (excluding core extensions that are mandatory).

JIPipe plugin manager

Environment EasyInstaller

In older JIPipe versions, external environments (Python, Cellpose, R, …) can be installed via prepackaged installation scripts that replicate the installation procedure that would be applied by a user. We were made aware of issues that are caused by updated to the software or differences in the system configuration. To simplify the installation of various environments, JIPipe now provides ready-to-used installation packages that can be simply downloaded and extracted via a user-friendly interface termed “EasyInstaller”.

Following EasyInstaller packages are available:

Cellpose EasyInstaller

TrackMate integration (Beta)

The TrackMate integration needs to be activated via the extensions manager. Go to 'Plugins > Manage JIPipe plugins' and activate the TrackMate extension.

TrackMate nodes

Using the TrackMate nodes

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tracking
simple
tutorial
A small example showcasing how to utilize the TrackMate nodes.

Cellpose integration

The Cellpose integration was rewritten to make use of the improved Cellpose CLI.

New Cellpose nodes

Omnipose integration (Beta)

The Omnipose integration needs to be activated via the extensions manager. Go to 'Plugins > Manage JIPipe plugins' and activate the Omnipose extension.

Based on the improved Cellpose integration, Omnipose was integrated using dedicated nodes. Please note that Omnipose is based on Cellpose 1.x and requires a dedicated environment.

Omnipose nodes

Using the Omnipose segmentation nodes

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segmentation
deep learning
simple
tutorial
A small example showcasing how to utilize the Omnipose nodes.

Image processing

ROI processing

There were various ROI-generating nodes with different feature sets. A new set of nodes was developed that make use of modern JIPipe API features. All nodes consume two optional inputs:

  1. ROI: Connect an existing ROI list to append to it. If left unconnected, a new ROI list is generated
  2. Reference: Connect an image to position ROI according to the image dimensions. If nothing is connected, the boundaries of the ROI provided by ROI is used, otherwise the width and height is assumed to be zero.

ROI drawing nodes

Coloc2 integration

Coloc2 node

Using the Coloc2 nodes

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colocalization
simple
tutorial
A small example showcasing how to utilize the Coloc2 nodes.

Table processing

Plotting

New plot nodes

General data processing

Parameters

New parameter table editor

Advanced parameters panel

Expressions

Node examples

In previous JIPipe versions, various nodes included a “Load example” button that allowed users to learn about how to utilize the node. An issue with this functionality is that it cannot be easily discovered by users, e.g., via the search box. Additionally, examples cannot be created and distributed by users due to the reliance on Java code. The new version of JIPipe introduces a standardized node example system that can dynamically load examples from files, JAR resources, and node templates.

Node examples

User interface

Project management

By default, JIPipe uses the repository https://raw.githubusercontent.com/applied-systems-biology/JIPipe-Repositories/main/project-templates/project-templates.json. Feel free to configure the repository list within Project > Application settings > General > Projects > Template downloader repositories

New project template downloader

Parameters

In older JIPipe versions, the help of a parameter was displayed upon hovering the item via the mouse. This lead to issues with usability, as well as a slowdown of the interface due to the involvement of performance-intensive Java functions. Since this version, the parameter documentation can be opened by clicking the ? icon next to the entry.

New parameters editor

Graph editor

Compartment editor

Improved compartment editor

Cache browser / Results viewer

New cache browser UI

ImageJ alias menu

To facility the transition from ImageJ, a function was introduced to organize JIPipe functionality into different menu locations (alias). Various existing JIPipe nodes were organized into a menu “IJ” that follows the structure of the ImageJ menu. For example, Images > Threshold > Auto Threshold 2D is also organized into IJ > Image > Adjust > Auto threshold ....

IJ alias menu

Image viewer

ROI manager

New ROI manager

Measurement tool / mask drawer / ROI drawer

New measurement tool

Plot editor

Table editor

New table editor

Dependency management

On loading pipelines with missing dependencies, users are prompted with dialogs to indicate that extensions are missing.

Node templates

Data management

Due to the improved data exporter interface, some parameters were deleted. Please evaluate the parameters of “Export data”/“Export images”/“Export table”

Data API

Bugfixes and small improvements

Please refer to the commits in the JIPipe GitHub repository to find a list of all bugfixes and improvements.

Known issues