This plugin extracts region of interest from pathology slides given their coordinates in an .xml file (by a pathologist) and save them in a separated image. It aslo creates corresponding mask based on annotations in the region of interest.
- Open the WSI image in Sedeen Viewer.
- Select the “RoiCropper” plugin from the pulldown list of Algorithms.
- Select “Region of Interest” in Parameters section (for example Region 55).
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Push the Run Bottom.
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Enter the name of whole slide image (for example 99797) and save it.
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The cropped region saves in the same path of original image with this naming format slideName_centreX_centreY_selectedRegion_crop.tif (for example: 99797_Region 55_23090_18015_crop.tif)
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The corresponding mask saves in the same path of original image with this naming format slidename_selectedRegion_centreX_centreY_mask.tif (for example: 99797_Region 55_23090_18015_mask.tif)
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The xml file which has extracted information of selected ROI from original image with this naming format slideName_selectedRegion_centreX_centreY_key.xml (for example: 99797_Region 55_23090_18015_key.xml).
RoiCropper Plugin was developed by Shiva Zaboli, Martel lab at Sunnybrook Research Institute (SRI), University of Toronto and was partially funded by NIH grant.
Copyright (c) 2019 Sunnybrook Research Institute
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