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bioimage-analysis

Microscopy image analysis for cell biology. Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization. For pathology WSI use pathml; for flow cytometry use flow-cytometry-analysis.

backend/cli/skills/biology/bioimage-analysis/SKILL.md

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# Bioimage Analysis: Microscopy Image Analysis for Cell Biology

## Overview

Bioimage Analysis provides computational tools for processing and quantifying microscopy images in cell biology research. From cell segmentation using deep learning (Cellpose) and classical methods (watershed, Otsu thresholding) to object tracking across time-lapse sequences, morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization. This skill covers the full pipeline from raw microscopy images to quantitative measurements suitable for statistical analysis.

## When to Use This Skill

- Segmenting cells or nuclei from brightfield or fluorescence microscopy images
- Tracking cell migration or particle movement in time-lapse sequences
- Quantifying cell morphology (area, eccentricity, circularity, aspect ratio)
- Counting bacterial or mammalian cell colonies on plates
- Analyzing colocalization of proteins from multi-channel fluorescence images
- Characterizing cytoskeleton fiber orientation and alignment