How to load and run projects – JIPipe for ImageJ

Summary

Explains how to load example projects into JIPipe.

Step 1

If you downloaded a *.zip file, please extract it first
Open JIPipe
Navigate to Project > Open

Step 2

Select a file that ends with *.jip
Click Open

Step 3

You will have two options:

This window will open the project in the current window
New window will create a new JIPipe window for the project

Choose the option that is most convenient for you.

Afterwards, the project will be opened in the JIPipe editor.

To execute the pipeline, you have two options:

Running the whole pipeline: 👉 this is recommended for running finalized pipelines on the full dataset
Caching specific nodes or compartments: 👉 use this option if still want to modify the pipeline or want to review intermediate results

Multiple options

There are multiple options to run a pipeline.

Running the whole pipeline
Running specific nodes

Step 4

To run the whole pipeline, click the Run button at the top right.

Info

Running a pipeline will store the results to the hard drive. While the generated directory structure can be browsed by humans, it is mainly designed to be opened by the JIPipe result browser.
If you want to re-open a generated results directory, navigate to Project > Open analysis output
If you intend to export files in a form that is more suitable for humans, please check out our tutorials.

Step 5

Please choose an empty output directory or leave the default setting (temporary folder).

Proceed by clicking Run now.

Step 6

You now can browse through the generated results.

Double-click items to open them in JIPipe or ImageJ (depending on the data type).

Step 2

To run a specific node or compartment, click the ⏵ button that is located on the node. Afterwards, select one of the options:

Update cache will run the pipeline up to the selected node and store only the results of the selected node
Cache intermediate results will run the pipeline up to the selected node, but also store all results of all predecessors

Choose the option that is most convenient for you.

Step 3

You now can browse through the generated results.

Double-click items to open them in JIPipe or ImageJ (depending on the data type).