trame-slicer 1.4.0

trame-slicer library

trame-slicer

trame-slicer is a Python library bringing 3DSlicer components in trame as a composable library.

It uses 3D Slicer's python wrapping and adds a thin wrapping to make it available with the trame framework.

Warning

As the 3D Slicer Python wheel is not yet generated by the 3D Slicer CI, manually generated wheels are provided for Python 3.10 for Windows and Linux WSL.

The API has not been stabilized / reviewed by the 3D Slicer core developers so please use this library with caution.

Downloading the latest wheels

Links to the latest VTK MRML wheels necessary to use this library in a Python environment can be downloaded here:

• Windows
• Linux

To use the library with other platforms (and Python 3.12), you can use the Slicer Trame module directly available in the Slicer 5.9+ extension manager.

Installing

The library can be installed as follows :

• Setup a Python 3.10 environment
• Activate your environment
• From PyPI
  • Use pip install trame-slicer to install the latest release
• From GitHub
  • Git clone the library
  • cd into the library
  • Use the pip install -e . command to install the library along it's dependencies
• Copy the vtk_mrml wheel file matching your OS (see Downloading the latest wheels)
  • Windows: pip install vtk_mrml-9.4.0-cp310-cp310-win_amd64.whl
  • Linux: pip install vtk_mrml-9.4.0-cp310-cp310-manylinux_2_35_x86_64.whl

Getting started

To get started using trame, please have a look at the introductory trame course.

To start using the trame-slicer library, have a look and run the medical viewer app

Features

The following subset of 3D Slicer features are currently supported :

• (limited) file loading
• Volume files (DCM, NRRD, NIFTI, ...)
• Model files (STL, OBJ)
• MRML / MRB files
• Segmentations (NRRD, NIFTI, ...)
• Display
  • 2D/3D with 3D Slicer UI manipulation
  • Volume Rendering preset / shift
• Bare bone access to 3D Slicer MRML scene and Core logic components

Work in progress

To make it easier for users to use trame-slicer, the following work are in progress :

• Slicer wheel generation merge into 3D Slicer's preview release
• CI changes to build the Slicer wheel along 3D Slicer's release
• 3D Slicer extension to install trame-slicer and launch a trame-slicer server directly from 3D Slicer

Troubleshooting

If you get the following error on Linux:

ImportError: cannot import name 'vtkMRMLDisplayableNode' from 'slicer' (XXX/lib/python3.10/site-packages/slicer/__init__.py)

You might be using a statically compiled Python. Please switch to a shared version of Python.

Contributing

Contributions are welcomed, please follow the CONTRIBUTING.md file for more information.

License

The library is distributed with a permissive license. Please look at the LICENSE file for more information.

Acknowledgment

This library was funded by the following projects :

• Cure Overgrowth Syndromes (COSY) RHU Project (ANR-18-RHUS-005).
• Handling heterogeneous Imaging and signal data for analysing the Neurodevelopmental Trajectories of premature newborns (HINT) ANR project (ANR-22-CE45-0034)

This library was created from the trame-cookicutter library.

Contact

If you are interested in learning how you can use trame-slicer for your use case in the near future, or want to get an early start using the framework, don't hesitate to contact us. Or reach out in the issue tracker and 3DSlicer discourse community.