SlicerPipelines is an extension for 3D Slicer for creating and executing simple modules (aka pipelines) via a GUI interface with no coding knowledge needed.
The SlicerPipelines extension allows to create and execute simple linear workflows using the PipelineCreator and the PipelineCaseIterator modules.
The design and implementation of this extension was initially motivated to simplify the creation of shape analysis workflow specific to the SlicerSALT community.
- Simple: Create and execute pipelines with a few clicks.
- Composable: Pipelines are themselves modules available as "steps" to create new pipelines.
- Extensible: Regular Slicer module modules, python functions, or executable can be registered as pipeline steps.
| Name | Description |
|---|---|
| PipelineCreator | Allows for the creation of pipelines via a GUI interface. |
| PipelineCaseIterator | Allows for automated running of a pipeline over all files in a directory via a GUI interface |
| PipelineModules | Support the registration of "wrappers" providing the steps used in the creation of pipelines by the PipelineCreator module. |
| PipelineCLIBridge | Bridge the gap between the CLI C++ interface and the Python code of the PipelineCreator. |
- To add steps to your pipeline, press the Insert Module button in the
Pipeline Creator. This will show a window where you can select the item you want to add. - Pick the item you want, fill in its parameters, and then select the next item in the pipeline.
- You need to repeat this process until the pipeline has all the steps in your workflow.
- Once all the steps have been appropriately captured in your pipeline interface, you can fill in the remaining fields like name and output directory.
- Press Finalize and the pipeline will be created.
💡 You should be able to find your new pipeline in the modules dropdown under a Pipeline Modules folder, as well as in the Insert Module pop up of the Pipeline Creator, so you can use the new module as a piece in a future pipeline.
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PipelineCreator depicting a pipelines composed of three SegmentEditor steps Thresholding, Smoothing and Island. |
Popup dialog for adding a pipeline step in the PipelineCreator module. |
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PipelineCaseIterator showing the progress toward the execution of a pipeline over 27 cases. |
To learn more about Slicer, SlicerSALT, and Slicer extensions, check out the following resources.
- https://slicer.readthedocs.io/en/latest/
- https://salt.slicer.org/
- https://slicer.readthedocs.io/en/latest/user_guide/extensions_manager.html
This software is licensed under the terms of the Apache Licence Version 2.0.