Download JIPipe 2.0.0

The version was pushed to 2.0.0 according to Semantic Versioning due to breaking changes in the Java API and OMERO integration.

This version focuses on improving the UX, OMERO support, and fixing issues.

Upgrade notes

Users

Developers

Input manager

In previous JIPipe versions, information and settings regarding the assembly of data batches was provided for each functional node in a tab “Data batches”. Users reported that the provided guidance was inadequate and confusing.

The design and functionality of the “Data batches” tab was fully overhauled and it was renamed to “Input manager” to better indicate the purpose of the panel.

The input manager is structured into three sections:

  1. Input data: An overview of the input data, annotations, and to which iteration step (data batch) the data is assigned
  2. Settings: The data batch generation settings (now renamed to “Input management”). By default only the most important parameters are displayed
  3. Preview iteration steps: Preview of the data batches as in previous versions

input-manager.png

Input data

Displays an overview of the node’s inputs, text annotations, and assigned iteration steps.

input-manager-input.png

Settings

The settings view allow to change the behavior of the algorithm that generates iteration steps. For example, it is possible to group data by custom columns.

input-manager-settings-1.png

👉 By default, only the most important settings are displayed. Select the “Advanced settings” checkbox to display all settings

input-manager-settings-2.png

Preview iteration steps

As in previous versions, the generated iteration steps (data batches) will be displayed as table.

The table now additionally provides color-coding consistent with the “Input data” view.

input-manager-preview.png

Other improvements

It is now better indicated what a user should do if no cached data is available. The naming was also made consistent with node context menus.

input-manager-missing-cached-data.png

Trace data

JIPipe now includes a function that allows you to trace the predecessors and successors of a specific data item. This function was requested to simplify the debugging process.

🛈 Not all nodes might be fully compatible yet with the data tracing and might break the tracing chain

The trace function can be triggered by right-clicking data in the cache browser or input manager and selecting “Trace”

data-trace-button.png

This will open a window that displays the known predecessors and successors of the selected data (highlighted in green). The interface allows you to display the data by double-clicking the items. You can also right-click items to open a context menu with more options.

data-trace.png

You can click the buttons at the top of each table to quickly navigate to the referenced node.

data-trace-goto.png

OMERO

The OMERO support was fully redesigned.

⚠ Many of the changes break existing OMERO-based workflows, so if you are relying on the OMERO integration as implemented in previous JIPipe versions, we recommend to stay in version 1.81.0.

Environment-based configuration

The previous version of OMERO integration was developed before the introduction of the JIPipe environment system that allows to easier manage different configurations of external tools or credentials. The new OMERO extension moved all server-related settings to the environment system to make it easier to connect to multiple servers.

omero-environment.png

omero-environment-2.png

New/reorganized nodes

Many OMERO nodes were redesigned and additional nodes were introduced.

omero-new-nodes.png

Other improvements

Expressions

The expression builder now has access to available annotations if the predecessor cache(s) are available. In future releases, this function will be expanded to more variable sources (e.g. table columns).

cached-expression-variables.png

Multi-data filtering nodes

It was not easily possible to filter related data (that are put into the same iteration step) without using data table data or data annotations. Two new nodes “Check iteration steps (one data per slot)”/”Filter multiple data by annotation (one data per slot)” and “Check iteration steps (multiple data per slot)”/”Filter multiple data by annotation (multiple data per slot)” were introduced to solve this issue.

The nodes are located in both the Miscellaneous and Annotations menus (via aliases) to improve findability.

multi-data-filtering-nodes.png

Redesigned montage nodes

The old montage nodes were severely limited and for example do not support 3D/4D/5D images. New nodes were designed that replace the old nodes (the old nodes were deprecated and are still functional).

The new montage nodes now support the following features:

new-montage-nodes.png

Minor improvements

UX

Bugfixes

Java API changes