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1. PhenoPixel PhenoPixel Public

   PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.

   Python 200 6

2. AbyssEye AbyssEye Public

   Microscopy workflow tool for TIFF datasets, ROI extraction, and AI-based analysis, developed with JAMSTEC and the authors of Nishimura et al. (Scientific Reports, 2025).

   TypeScript 81

3. kevinjohncutler/omnipose kevinjohncutler/omnipose Public

   Omnipose: a high-precision solution for morphology-independent cell segmentation

   Python 164 46