Loading and segmentation of histopathology imaging for radiological-pathological correlation

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  Projects List

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Key Investigators

• SPL: Tobias Penzkofer, Andrey Fedorov

Objective

To enable Slicer 4 to load, view and process histopathology data.

Approach, Plan

Find, analyze and adapt the routines responsible for 3 channel image handling to enable processing of scanned histology slides with possible extensions towards registration of histo/path, digital pathology imaging and analysis.

Specifically we would like to be able:

• loading / saving of Slicer scenes that contain RGB volumes
• masking and segmentation of RGB volumes in Editor

Progress

Possible solutions have been identified (Downsampling, NRRD file format save) and applied. Loose ends have been identified.

Bug report submitted: http://www.na-mic.org/Bug/view.php?id=2225

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

1. Slicer Module
   1. Built-in YES
   2. Extension -- commandline NO
   3. Extension -- loadable PROBABLY
2. Other (Please specify)

References

• Trivedi, H., B. Turkbey, et al. (2012). "Use of patient-­‐specific MRI-­‐based prostate mold for validation of multiparametric MRI in localization of prostate cancer." Urology 79(1): 233-­‐239.
• "Elastic registration of multimodal prostate MRI and histology via multiattribute combined mutual information." Med Phys 38(4): 2005-­‐2018.
• "Semi-­‐automatic deformable registration of prostate MR images to pathological slices." J Magn Reson Imaging 32(5): 1149-­‐1157.