KPIS_data

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.

Scripts description:

• 1. Save_geojson.groovy: This is used in QuPath, to export annotations as contours, then saved to JSON files with coordinates.
• 2. draw_contour_with4points_scn.py: This script is used for converting contours JSON file to binary mask.
• 3. KPIS_CZI_patchCrop.py: The script used to crop patches from CZI file.
• 4. movefile.py: Find only the patches with foregrounds, remove empty tiles.

Subject CZI read scenes:

• DN

  • 11-356: scene 0
  • 11-357: scene 1
  • 11-358: scene 0
  • 11-367: scene 0
  • 11-370: scene 0

• 56Nx

  • 12-116: scene 2
  • 12-117: scene 1
  • 12-169: scene 1
  • 12-170: scene 2
  • 12-171: scene 1

• Normal:

  • F4: scene 0
  • F2: scene 1
  • F1: scene 0
  • F3: scene 3
  • F1576: scene 1