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How to load and run projects

Explains how to load example projects into JIPipe.

This tutorial assumes that you have installed JIPipe. If you want information on how to setup our software, please visit the installation guide.

This guide was written for JIPipe version 1.74.0 or newer

Table Of Contents

Illustration of the tutorial step

Loading: Step 1

  1. If you downloaded a *.zip file, please extract it first
  2. Open JIPipe
  3. Navigate to Project > Open
Illustration of the tutorial step

Loading: Step 2

  1. Select a file that ends with *.jip
  2. Click Open

*.jip files are typically located either directly in the root directory of the package, or within a subdirectory ProtocolAndData.

Illustration of the tutorial step

Loading: Step 3

You will have two options:

  1. This window will open the project in the current window
  2. 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:

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

Running the whole pipeline: Step 1

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

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.

Illustration of the tutorial step

Running the whole pipeline: Step 2

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

Proceed by clicking Run now.

Illustration of the tutorial step

Running the whole pipeline: Step 3

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

Proceed by clicking Run now.

Illustration of the tutorial step

Running the whole pipeline: Step 4

You now can browse through the generated results.

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

If you want more information about the result browser, please visit the result browser documentation.

Illustration of the tutorial step

Running/caching nodes: Step 1

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

  1. Update cache will run the pipeline up to the selected node and store only the results of the selected node
  2. 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.

Illustration of the tutorial step

Running/caching nodes: Step 2

You now can browse through the generated results.

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

If you want more information about the cache browser, please visit the tutorials.