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README.md
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- Batch size: 1
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- Framework: Cellpose 4.x (`train.train_seg`)
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- Hardware: NVIDIA GPU (CUDA 12.6)
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## Intended use
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Segmentation of bacteria (~1.5 µm) in Airyscan confocal images of mouse colon tissue for downstream fluorescence ratio measurements (GFP/BFP osmotic stress, RFP/BFP oxidative stress reporters).
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Post-segmentation filters recommended:
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1. Size filter: 8–300 px²
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2. Spectral filter: remove objects where min(GFP, RFP) / BFP > 0.6 (fecal autofluorescence)
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3. SYTOX exclusion: remove objects overlapping > 25% with SYTOX+ host nuclei
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- Batch size: 1
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- Framework: Cellpose 4.x (`train.train_seg`)
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- Hardware: NVIDIA GPU (CUDA 12.6)
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