README.md

QuPath_Annotation_to_AnnData

Annotate cells whether they are inside a QuPath annotation.

Inputs: QuPath geojson export of annotations. Anndata object to annotate.

Output: New column in adata.obs, called ROI, where the name of the QuPath Annotation will be, as a string.

Potential issues:

1. What about a cell being inside two ROIs?

QuPath_Annotation_to_Quantification_file

Running with Docker:

• inputs:
  • quantification file (csv) with columns: X_centroid, Y_centroid
  • geojson file with annotations
• outputs:
  • quantification file with new column: ROI
  • optional qc png files for each ROI

Pull docker image:

docker pull kbestak/ann_to_quant:0.1.0

Run command:

docker run \
    -v /path/to/inputs:/data \
    -v /path/to/outputs:/output \
    kbestak/ann_to_quant:0.1.0 \
    python run_annotation.py \
    --in-quantification ../data/quantification.csv \
    --in-annotation ../data/annotations.geojson \
    --out ../output/quantification.csv \
    --qc ../output/qc

Provided Dockerfile (replace CRLF with LF) is for building the image locally from the environment.yml file (replace CRLF with LF).