QuPath GeoJSON Converter from ArtidisNET

Initial release of QuPath GeoJSON Converter, a lightweight graphical tool for converting GeoJSON annotation files into QuPath-compatible formats.

Main features

• Convert single or multiple GeoJSON files.
• Select files manually or process all GeoJSON files from a folder.
• Optional recursive folder processing.
• Save converted files in the original location or in a user-selected output folder.
• Preserve extra metadata fields when needed.
• Option to overwrite existing converted files.
• Progress bar during conversion.
• Error log shown only when conversion errors occur.
• Simple cross-platform GUI built with Python and Tkinter.

Conversion modes

This release includes five conversion modes:

1. Merge into one annotation per class
   Creates one QuPath annotation for each class by merging geometries that share the same class name.

2. Standard QuPath annotations
   Converts each input GeoJSON feature into a QuPath annotation without merging, splitting, or converting it into an object.

3. Create individual QuPath objects for counts
   Converts each input feature into an individual QuPath detection/object, useful for class-specific object counting.

4. Create class annotations + individual objects
   Creates class-level annotations while also preserving individual objects for counting.

5. Split MultiPolygon into individual Polygon features
   Splits MultiPolygon geometries into separate Polygon annotations, which may help with complex geometries during import into QuPath.

Input and output

The tool converts external GeoJSON classification fields such as:

{
  "class_name": "Neoplastic Tissue",
  "class_color_hex": "#FF0100"
}

into QuPath-compatible properties:

{
  "objectType": "annotation",
  "classification": {
    "name": "Neoplastic Tissue",
    "color": [255, 1, 0]
  }
}

Converted files are saved with the suffix:

_qupath.geojson

Example:

LS026 HE.geojson
LS026 HE_qupath.geojson

Notes

This is an independent utility and is not affiliated with or endorsed by the QuPath project.