Data processing utilities for KPIS Challenge
TODO: we need to define end-to-end workflow for data curation. Currently, we use several scripts for processing raw data.
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Save_geojson.groovy
: This is used in QuPath, to export annotations as contours, then saved to JSON files with coordinates.
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draw_contour_with4points_scn.py
: This script is used for converting contours JSON file to binary mask.
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KPIS_CZI_patchCrop.py
: The script used to crop patches from CZI file.
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movefile.py
: Find only the patches with foregrounds, remove empty tiles.
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DN
- 11-356: scene 0
- 11-357: scene 1
- 11-358: scene 0
- 11-367: scene 0
- 11-370: scene 0
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56Nx
- 12-116: scene 2
- 12-117: scene 1
- 12-169: scene 1
- 12-170: scene 2
- 12-171: scene 1
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Normal:
- F4: scene 0
- F2: scene 1
- F1: scene 0
- F3: scene 3
- F1576: scene 1