PhenoPixel

PhenoPixel is a FastAPI + React application for microscopy single-cell extraction, annotation, visualization, and batch phenotype analysis. It is designed around ND2 microscopy workflows: upload an ND2 file, extract cell contours, clean labels, inspect individual cells, and export population-level shape and fluorescence descriptors. The montage below shows a label-1 cell population from microscope_data.db. The overlay renders fluo1 as magenta and fluo2 as green without scale bars, with display intensity balanced per cell while avoiding saturation. Run the backend and frontend from the repository root in separate terminals. The local quick-start path uses python3.14; the Docker backend image uses Python 3.11. PhenoPixel is the open-source project ikeda042/PhenoPixel (https://github.com/ikeda042/PhenoPixel) by ikeda042, released under MIT. Ion packages it unmodified from commit 20b42196fd9a, adding only a manifest, an icon and a start script.

Written by ikeda042, published to Oikou by Ben Grande.

• ★ 200 stars on GitHub
• Licence: MIT
• Upstream version v0.1.0
• Built from commit 20b42196fd9a

View the repository on GitHub

Not rated. Nobody has said who this app is suitable for, so Personal Clouds and the Oikou app treat it as 18+.

Internet

It asks to reach nothing on the internet.

Personal Cloud tools

None. It uses nothing from your Personal Cloud beyond its own storage.

Notifications

It does not send push notifications.

Storage

Up to 512 MB on your Personal Cloud.

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