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.

Usage

The API Reference documentation provides API-level documentation.

Installing

The library can be installed in a Python environment as follows:

• Setup a Python 3.10-3.13 (included) virtualenv and activate it
• From PyPI
  • Use pip install "trame-slicer[standalone]" to install the latest release
• From GitHub
  • Git clone the library
  • cd into the library
  • Use the pip install -e ".[standalone]" command to install the library along it's dependencies
• For optimal performances, you should install turbo-jpeg

Optional dependencies

• vtkstreaming: install trame-slicer[vtkstreaming] to enable RCA video encoding. Without it, requesting the video encoder (with rca_encoder="video") will fall back to JPEG image encoding.

Encoding

Views are streamed to the browser using the encoder given to register_rca_factories / RemoteViewFactory through the rca_encoder parameter:

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:

python -m trame_slicer.app.medical_viewer_app

Features

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

Views

• 3D view
  • Volume rendering
  • Color presets / shift
• 2D/slice view
  • Scroll/Zoom/Pan
  • Window Leveling (W/L)
  • Multiplanar Reformation (MPR)
  • Slice/slab thickness (MIP, MinIP, AvergageIP)
• Any other view types (e.g. plotly)

Layouts

• Conventional, four-up, side-by-side
• Fullscreen mode
• Custom layouts

I/O

• DICOM
  • MRI, CT, US, XR, PET, DWI…
• Scalar volumes
  • NRRD, NII, TIFF, HDR, IMG, MHA…
• Segmentation
  • SEG.NRRD, NRRD, SEG.NHDR, NHDR, NII, NII.GZ, HDR…
• Models/Meshes
  • OBJ, STL, VTK, VTP…
• 3D Slicer scene
  • MRML, MRB

Segmentation tools

• Paint: free-hand brush, 2D or 3D, varying radius
• Erase: invert paint
• Scissors: 2D or 3D sculpting
• Draw: fill the area of a drawn contour
• LogicalOperators: binary combination of segments
• Threshold: create segment based on intensity values
• Islands: keep largest, smallest… connected-components
• Smoothing: apply gaussian blur on existing segments
• Volume Intensity Masking: define a ROI with threshold where other segmentation tools work into
• Undo/Redo

Markups

• Fiducials/points
• Ruler/lines
• Angle
• Open curve/spline
• Close curve
• Plane
• ROI/box

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

ERROR: No matching distribution found for slicer-core

slicer-core is only supported on specific platforms, please check that your OS and Python version are listed on pypi

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.

Acknowledgments

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.