CellProfiler/CellProfiler
An open-source application for biological image analysis observed · 2026-09-01
Health v2 · maintenance only
68/100
- Activity 100
- Release rhythm 8
- Longevity 100
Flags: no_license
How is this computed?
round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10) — computed 2026-09-03. Adoption (stars, forks) is never an input.
- gap_med: n/a
- age_days: 5629
- days_rel: 705
- days_push: 2
- n_releases_24m: 1
Adoption not part of the score
1135 stars · 423 forks observed · 2026-09-01
What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded
CellProfiler is a free, open-source desktop application for quantitative analysis of biological images, letting biologists build modular image-processing pipelines without programming. It can automatically measure phenotypes from thousands to millions of images and export results to spreadsheets or databases.
Use cases
- measure cell phenotypes from microscopy images
- count and segment cells in fluorescence images
- batch-process thousands of biological images automatically
- build image analysis pipelines without coding
- quantify high-content screening assay images
- export image measurements to a spreadsheet or database
- classify cell phenotypes with machine learning via CellProfiler Analyst
When to choose
- you are a biologist needing quantitative image measurements without programming
- you need reproducible, modular pipelines for large batches of microscopy images
- you want a mature GUI tool for cell segmentation and feature measurement
When to avoid
- you need general-purpose computer vision development rather than biological image analysis
- you require a headless library to embed in your own Python code (consider cellprofiler-core or other libraries)
- you need real-time image processing
Facets
application · maturity active
image-processing computer-vision machine-learning gui data-science bioinformatics image-processing data-science healthcare windows python cross-platform biological-imaging phenotype-analysis high-content-screening image-analysis-pipelines microscopy macos linux
7 sources
- readme: https://github.com/CellProfiler/CellProfiler · fetched 2026-09-01 · cae7c9ced3be
- homepage: http://cellprofiler.org · fetched 2026-08-29 · b590763d56bf
- site_page: https://cellprofiler.org/about · fetched 2026-08-29 · bb67a0a2eaf1
- site_page: https://cellprofiler.org/getting-started · fetched 2026-08-29 · 96625b4b0756
- registry_pypi: https://pypi.org/pypi/cellprofiler/json · fetched 2026-08-29 · faab72d75b61
- site_page: https://cellprofiler.org/releases · fetched 2026-08-29 · 4268553e6474
- site_page: http://cellprofiler.org/releases · fetched 2026-08-29 · dab24968caad
Member repositories
| Repository | Role | Health v2 |
|---|---|---|
| CellProfiler/CellProfiler | main | 68 |
For agents
markdown · JSON · MCP: product_card(name="CellProfiler/CellProfiler")
Data as of 2026-08-30T08:39:29.467469+00:00 · Report a problem