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 data in a csv file via a GUI interface |
| PipelineModules | Support the registration of "wrappers" providing the steps used in the creation of pipelines by the PipelineCreator module. |
- To add steps to your pipeline, press the Add Step 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, it will be added as a step to your pipeline.
- For each parameter you decide wether you want its value to be fixed to a given value, refer to an output of a previous step, or be set by the user at runtime. You can add parameters to be set by the user by pressing the + button in
Step 0 - Inputs. - 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 Test Pipeline to make sure the pipeline is valid.
- Press Generate Pipeline 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 Add Step pop up of the Pipeline Creator, so you can use the new module as a piece in a future pipeline.
- Select the pipeline you want to run in the
Pipeline Case Iteratormodule. - Select the csv file containing the cases you want to run the pipeline on. If this is the first time you are running the pipeline, you can use the Template Parameter File button to create a stub csv file, for types that are nodes an path to the file should be given.
- Select the output directory where you want the results to be saved. The output directory will contain all the results of the pipeline, as well as a
.csvfile with the appropriate input and output parameters for each row. - Optionally select an output extension for the files generated by the pipeline. A prefix and suffix and an timestamp can also be added to the output files.
- Press Run to run the pipeline on all the cases in the csv file.
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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.