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NA-MIC Project Weeks

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Key Investigators

Project Description

CERRx is an Octave/MATLAB-based software platform for developing and sharing research results using radiation therapy treatment planning and imaging informatics. “sliCERR” is being developed to facilitate the use of CERRx’s radiotherapy and image analysis functionality. The extension we envision, “sliCERR”, will provide scripted modules for data I/O operations, and will run analysis routines from CERRx.


“sliCERR” will be a scripted module for Slicer, written in Python. We are starting in Jupyter notebooks with 3D Slicer kernel for visualization and image processing. The cerr2mrml module handles the I/O operations of loading native CERR planC format files into the 3DSlicer MRML scene, including import of scan, dose and ROI contours.

  1. Easy imaging data IO exchange between CERR and 3D Slicer platforms via module UI
  2. Enable CERRx features for dosimetry and image analysis, ROE Radiotherapy Outcomes Estimator, semi-quanitative DCE features, DL-based image segmentation models

Approach and Plan

  1. Slicer-Jupyter notebooks to code the data import/export process and analysis as proof-of-concept
  2. User interface was development for 3DSlicer GUI to simplify the process of selecting CERR-format datasets for import in 3DSlicer.

Progress and Next Steps

  1. Use of specialized functions in CERR such as Deep Learning-based image segmentation and radiomics texture mapping, demonstrated in Jupyter notebooks publicly available on GitHub.
  2. GUI is in development
  3. Expand wiki documentation for setup and usage


Link to Jupyter Notebook demo: https://mskcc.box.com/s/eizbm2nc54uvddcomzmvotw2w8sl82h4


planC with dose in Slicer

import DICOM to planC

Background and References