GeoJSON to TIFF

An entirely non-general tool to convert a GeoJSON set of polygons into a multi-resolution TIF image.

This code was written to convert polygons of nuclear segmentations (https://doi.org/10.1038/s41597-020-0528-1) to TIF images. It may need to be tweaked to work with other datasets.

The original polygons were converted to GeoJSON with the scidata-to-geojson.py script.

Example

Here I demonstrate using this within an Apptainer (formerly Singularity) container.

1. First, get the container. Feel free to swap out the apptainer command for singularity.

   apptainer pull docker://kaczmarj/geojson2tif:latest
   

2. Run the tool. You will need a GeoJSON file with the labels and the corresponding whole slide image.

   apptainer exec --pwd $(pwd) geojson2tif_latest.sif \
       --wsi image.tif --geojson polygons.json --output mask.tif
   

Installation

Use the Docker image for a hassle-free experience.

Otherwise, please install ASAP version 2.1 and wholeslidedata from commit 247c2429f90a47e42493d43d6bb94316b1179aa7.

If you need to use scidata-to-geojson.py, please install shapely as well.