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gitter-colony

gitter-colony is a Python 3.13 rewrite of the original R gitter package for quantification of pinned microbial colonies from plate images.

Start Here

  1. Install the package: Installation
  2. Run one image end-to-end in Python: Quick Start
  3. Learn the core functions: Python API

What You Can Do

  • Quantify colony sizes from a single image (gitter)
  • Split multi-plate images explicitly with PlateSplitter
  • Run batch quantification (gitter_batch)
  • Read/write CSV results (read_results_csv, write_results_csv)
  • Plot heatmap and bubble summaries (plot_results)
  • Validate biological agreement against original R output (static + live Docker tests)