> For the complete documentation index, see [llms.txt](https://rotsl.gitbook.io/rotsl/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://rotsl.gitbook.io/rotsl/projects/bio-imaging.md).

# Bio Imaging

This page collects my biological imaging and Petri-dish analysis work.

## Analysis pipeline

```mermaid
flowchart TD
    Images[Petri-dish images] --> Metadata[Image metadata]
    Images --> Crop[metrics-petri-crop]
    Crop --> Segmentation[Colony segmentation]
    Metadata --> Growth[Growth-rate calculations]
    Segmentation --> Morphometrics[Morphometric outputs]
    Morphometrics --> Exports[JSON and CSV exports]
    Morphometrics --> Charts[ggplot2 visuals]
    Growth --> Charts
    Exports --> Records[Dataverse and BioStudies records]
```

## grayleafspotr

Self-contained gray leaf spot analysis and plotting tools for RStudio. The package runs a SmallUNet segmentation pipeline (`models/best_area_w_0.7.pt`) via an ARM64 Python 3.11 environment, writes raw JSON and CSV exports, and provides template ggplot2 visuals for downstream exploration.

[![R-universe package](https://img.shields.io/badge/R--universe-grayleafspotr-276dc3?style=for-the-badge\&logo=r)](https://rotsl.r-universe.dev/grayleafspotr)

## metrics-petri

Petri dish colony segmentation and morphometric analysis.

Python package metrics-petri measures how a biological sample grows on a petri dish: area, diameter, edge roughness, crack burden, texture entropy, and time-series growth rates, all in physical units calibrated from the dish geometry.

The package also ships **metrics-petri-metadata**, a desktop GUI for creating the image metadata file used for growth-rate calculations and chart labelling, and **metrics-petri-crop**, a standalone dish cropper.

**metrics-petri-crop** automatically detects and crops individual Petri dishes from photos where several dishes were captured together in a single image (2-8+ per photo). It is a standalone utility, independent of the analysis pipeline.

[![GitHub repository](https://img.shields.io/badge/GitHub-Repository-24292f?style=for-the-badge\&logo=github)](https://github.com/rotsl/metrics-petri)

[![PyPI package](https://img.shields.io/pypi/v/metrics-petri?style=for-the-badge\&label=PyPI\&logo=pypi)](https://pypi.org/project/metrics-petri/)

[![PyPI downloads](https://static.pepy.tech/personalized-badge/metrics-petri?period=total\&units=INTERNATIONAL_SYSTEM\&left_color=YELLOW\&right_color=RED\&left_text=downloads)](https://pepy.tech/projects/metrics-petri)

[![Documentation](https://img.shields.io/badge/Open-Documentation-2f80ed?style=for-the-badge)](https://rotsl.github.io/metrics-petri/)

[![Dataverse DOI](https://img.shields.io/badge/Dataverse-10.7910%2FDVN%2FSR2HBR-facc15?style=for-the-badge)](https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/SR2HBR)

[![BioStudies DOI](https://img.shields.io/badge/BioStudies-10.6019%2FS--BSST3199-2f80ed?style=for-the-badge)](https://www.ebi.ac.uk/biostudies/studies/S-BSST3199)

DOI: 10.7910/DVN/SR2HBR on Harvard Dataverse: *metrics-petri: software for magnaporthe colony segmentation and morphometric analysis of petri-dish images*.

DOI: 10.6019/S-BSST3199 on BioStudies: *Time-series Magnaporthe colony images from twelve petri dishes and morphometric analysis results generated using metrics-petri 3.0.0*.

Source code is deposited in the Harvard Dataverse record above. The BioStudies record contains 49 original time-series Petri-dish images of *Magnaporthe* colonies from 12 plates, associated image-level metadata, and extracted morphometric analysis outputs generated using metrics-petri version 3.0.0.

## Related project

[![Automator](https://img.shields.io/badge/Open-Automator-2f80ed?style=for-the-badge)](/rotsl/projects/automator.md)