Weights for PUMA challenge

Baseline Solution Weights for the PUMA Challenge

• For PUMA-challenge-baseline-track1 the content of Hover-NeXt_3_classes needs to be placed in the checkpoint folder
• For PUMA-challenge-baseline-track2 the content of Hover-NeXt_all_classes needs to be placed in the checkpoint folder
• For both tracks the nnU-net/checkpoint_best.pth needs to be placed inside the folder:
  \nnunetv2\nnunetv2_hist\nnUNet_results\Dataset526_Mark\nnUNetTrainer_nnUNetPlans_2d\fold_4

Qupath Groovy Code for Importing a GeoJSON File

• To visualize all GeoJSON files:
  1. Create a project for the dataset.
  2. Import regions of interest into the project.
  3. In the project folder, create a new folder named "geojson".
  4. Move all GeoJSON files to this folder.
  5. Adjust line 7 of the script to specify either "_nuclei.geojson" for nuclei visualization or "_tissue.geojson" for tissue annotation visualization.
  6. Click "Run for project" to add annotations for all images 

Note: Running this script will remove all existing annotations from the files, so ensure that this step is done with caution.