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Update the Chest Imaging Platform extenstion to support Slicer 5

Key Investigators

Project Description

The Chest Imaging Platform (CIP) is an extension to 3D Slicer.

image

It integrates:

In the current preview versions of 3D Slicer (4.13.0) parts of CIP fail to load the following CIP modules because Slicer’s “Editor” module has been removed.

CIP_CalciumScoring

CIP_RVLVRatio

CIP_LesionModel

CIP_Calibration

CIP_MIPViewer

CIP_BodyComposition

CIP_ParenchymaSubtypeTrainingLabelling

CIP_ParenchymaAnalysis

CIP_PAARatio

CIP_AVRatio

CIP_InteractiveLobeSegmentation

The CIP extension currently uses legacy editor module, and charts infrastructure (instead of Segment editor, Plots, and Tables modules).

Objective

Approach and Plan

A fork and branch of SlicerCIP was created at https://github.com/rbumm/SlicerCIP/tree/Branch_CIPCompatSlicer5 to be used as the source base, all changes will later be included in a PR to https://github.com/acil-bwh/SlicerCIP.

Resolve compatibility problems step by step

Deactivate non-working or outdated modules in Slicer 5

Considerations

Progress and Next Steps

01/06/22:

Removing the “Editor” related imports from “Scripted/CIP_/CIP/ui/init.py” results in a complete CIP-startup in Slicer 4.13.0 without initial error messages.

A github search revealed that “Editor” calls are being made from three of the above modules:

01/11/22:

01/17/22: 12pm Meeting with Raul, Andras, Steve and Rudolf (Discord Red Slice)

01/18/22: 12pm Meeting with Raul, Andras, Rudolf (Discord Red Slice)

Final presentation start here

01/20/22: 11am-12:30pm Meeting with Raul, Andras, Rudolf (Discord Red Slice)

Illustrations

New Slicer 5 CIP “Calibration” module with embedded “SegmentEditor” instead of the old “Editor”:

image

Background and References

https://chestimagingplatform.org/

https://discourse.slicer.org/t/exporting-csv-with-parenchyma-analysis-module/10697/58?u=rbumm