{"repo":"ikeda042/PhenoPixel","free":true,"listed":false,"github":"https://github.com/ikeda042/PhenoPixel","clone":"git clone https://github.com/ikeda042/PhenoPixel.git","description":"PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.","language":"TypeScript","stars":238,"topics":["bacteria","bioinformatics-pipeline","cell-analysis","fastapi","fluorescence-microscopy-imaging","microbiology","opencv","react","single-cell-analysis","cell-contour"],"license":"MIT","category":"analytics","readme_excerpt":"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. Key Features Area What PhenoPixel provides --- --- ND2 management Upload, list, inspect metadata, download, delete, and parse .nd2 files. Cell extraction Generate cropped cell images, contours, preview frames, and SQLite databases. Annotation Review auto-detected cells and relabel single cells or debris in bulk. Cell viewer Inspect phase, fluorescence, overlays, replot views, heatmaps, map views, distributions, and raw images per cell. Bulk analysis Export and visualize cell length, area, fluorescence intensity summaries, heatmap vectors, contours, Map256 strips, raw intensities, and JSON/CSV data. Research reporting Keep database files, exports, screenshots, and method formulas close to the analysis code for reproducible reporting. Requirements Component Notes --- --- Python Local launch examples use python3.14 ; the Docker backend image uses Python 3.11. Node.js / npm Required for the React frontend, Docusaurus docs bu","default_branch":null,"files":null,"tree":[],"storefront":"/r/ikeda042","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/ikeda042/PhenoPixel/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}