| --- |
| license: mit |
| tags: |
| - image-segmentation |
| - histology |
| - biology |
| - unet |
| - cellpose |
| --- |
| |
| # dpc_im — Mouse Skin H&E Segmentation Models |
| |
| Fine-tuned models for semi-automated segmentation of mouse skin layers and hair follicles from H&E histology images. Part of the [dpc_im](https://github.com/SolomonLalala/dpc_im) pipeline. |
| |
| ## Models |
| |
| | File | Task | Base model | Training images | |
| |---|---|---|---| |
| | `best_model.pth` | 5-class layer segmentation (background, dermis, epidermis, adipose, muscle) | [U-Net ResNet34](https://github.com/qubvel/segmentation_models.pytorch) — ImageNet | 5 annotated mouse skin H&E images (1920×1440 px, 4×, 7.615 µm/px) | |
| | `cellpose_hf_best` | Hair follicle instance segmentation | [Cellpose SAM](https://github.com/MouseLand/cellpose) | 8 train + 2 val annotated mouse skin H&E images (1920×1440 px, 4×, 7.615 µm/px) | |
|
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| ## Usage |
|
|
| See [dpc_im](https://github.com/SolomonLalala/dpc_im) for installation and full pipeline usage. |
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|
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| ## Citation |
|
|
| Pachitariu, M., Rariden, M., & Stringer, C. (2025). Cellpose-SAM: superhuman generalization for cellular segmentation. *bioRxiv*. https://doi.org/10.1101/2025.04.03.647135 |
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|
| Iakubovskii, P. (2019). Segmentation Models Pytorch. GitHub. https://github.com/qubvel/segmentation_models.pytorch |
| |
