gitter-colony 1.2.1

Python port of the gitter colony quantification pipeline.

gitter-colony

Python 3.13 rewrite of the original R gitter package for quantification of pinned microbial colonies.

Documentation: https://cyberstefnef.github.io/gitter-colony/

Installation

Install with pip:

pip install gitter-colony

Install with uv:

uv add gitter-colony

Python Usage (Recommended)

from gitter_py import gitter, plot_gitter

df = gitter(
    image_file="examples/extdata/sample.jpg",
    plate_format=1536,
    verbose="n",
)

fig = plot_gitter(df, plot_type="heatmap", title="Sample")
fig.savefig("sample.png", dpi=200)

CLI (Optional)

gitter run examples/extdata/sample.jpg --plate-format 1536 --grid-save . --dat-save .
gitter read sample.jpg.dat
gitter plot sample.jpg.dat --plot-type heatmap --out sample.png

Live R Parity Test (Optional)

docker build -t gitter-r-parity:4.3.3 -f docker/r-parity.Dockerfile .
GITTER_ENABLE_R_LIVE=1 uv run --extra dev pytest -q -m r_live tests/test_parity_r_live.py