QuPath instanseg extension

Development setup:

• Clone Alan's qupath fork https://github.com/alanocallaghan/qupath
  • If you have the main qupath repo cloned already, you could add it as a remote git add remote alan git@github.com:alanocallaghan/qupath.git && git fetch alan
  • If you want to make a fresh clone, then continue, the following instructions should still work
  • Switch to branch instanseg
    • If you added a remote, then git checkout instanseg
• Clone this repo in the same directory as qupath, eg
  • git clone git@github.com:qupath/qupath-extension-instanseg.git
  • git clone git@github.com:qupath/qupath-extension-djl.git
• Enter the qupath folder cd qupath
• Run QuPath using ./gradlew run
• Open extension (extensions -> run instanseg)
• Enter the path to the model .pt file(s) in "Downloaded model directory"
• Choose appropriate device/thread/tile size settings
• Run...?