Loading and segmentation of histopathology imaging for radiological-pathological correlation

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  Projects List

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Key Investigators

• SPL: Andrey Fedorov, Tobias Penzkofer

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: loading / saving of RGB volume containing scenes, masking and segmentation of RGB scenes (Editor).

Progress

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

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.