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Update README.md with more cellpose models #7

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Update README.md with more cellpose models #7

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8395f34
Update README.md with more cellpose models
aemmav Aug 2, 2024
091ba7a
Update __init__.py
aemmav Aug 5, 2024
37ee7c0
Merge branch 'aemmav-patch-1' into aemmav-patch-2
rhoadesScholar Aug 5, 2024
64018aa
Merge pull request #8 from janelia-cellmap/aemmav-patch-2
rhoadesScholar Aug 5, 2024
8f047c6
Update __init__.py
aemmav Aug 6, 2024
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29 changes: 29 additions & 0 deletions src/cellmap_models/pytorch/cellpose/README.md
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Expand Up @@ -10,22 +10,51 @@ This directory contains scripts for downloading finetuned Cellpose models, parti

**jrc_mus-epididymis-2_nuc_cp:**

**jrc_mus-granule-neurons-1_nuc_cp:** Cellpose was trained on nuclei from 12 2D slices from jrc_mus-granule-neurons-1.

**jrc_mus-granule-neurons-2_nuc_cp:** Cellpose was trained on nuclei from 10 2D slices from jrc_mus-granule-neurons-2.

**jrc_mus-granule-neurons-3_nuc_cp:** Cellpose was trained on nuclei from 21 2D slices from jrc_mus-granule-neurons-3.

**jrc_mus-guard-hair-follicle_nuc_cp:** Cellpose was trained on nuclei from 22 2D slices from jrc_mus-guard-hair-follicle.

**jrc_mus-heart-1_ecs_cp:**

**jrc_mus-heart-1_nuc_cp:**

**jrc_mus-hippocampus-1_nuc_cp:**

**jrc_mus-kidney_nuc_cp:** Cellpose was trained on nuclei from 28 2D slices from jrc_mus-kidney.

**jrc_mus-kidney-2_nuc_cp:** Cellpose was trained on nuclei from 38 2D slices from jrc_mus-kidney-2.

**jrc_mus-kidney-3_nuc_cp:**

**jrc_mus-liver-2_nuc_cp:** Cellpose was trained on nuclei from 29 2D slices from jrc_mus-liver-2.

**jrc_mus-liver-3_nuc_cp:**

**jrc_mus-meisnner-corpuscle-1_nuc_cp:** Cellpose was trained on nuclei from 21 2D slices from jrc_mus-meisnner-corpuscle-1.

**jrc_mus-meisnner-corpuscle-2_nuc_cp:** Cellpose was trained on nuclei from 27 2D slices from jrc_mus-meisnner-corpuscle-2.

**jrc_mus-pacinian-corpuscle_nuc_cp:** Cellpose was trained on nuclei from 31 2D slices from jrc_mus-pacinian-corpuscle.

**jrc_mus-pancreas-1_nuc_cp:** Cellpose was trained on nuclei from 34 2D slices from jrc_mus-pancreas-1.

**jrc_mus-pancreas-2_nuc_cp:** Cellpose was trained on nuclei from 30 2D slices from jrc_mus-pancreas-2.

**jrc_mus-pancreas-3_nuc_cp:** Cellpose was trained on nuclei from 4 2D slices from jrc_mus-pancreas-3.

**jrc_mus-pancreas-4_nuc_cp:** Cellpose was trained on nuclei from 17 2D slices from jrc_mus-pancreas-4.

**jrc_mus-skin-1_nuc_cp:**

**jrc_mus-thymus-1_nuc_cp:**

### Trained on fly tissues
**jrc_fly-mb-z0419-20:** Cellpose was trained on nuclei from 32 2D slices from jrc_fly-mb-z0419-20.

## Usage

Once you have chosen a model based on the descriptions above, you can download its weights from the `cellmap-models` repository and use them as described below:
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14 changes: 14 additions & 0 deletions src/cellmap_models/pytorch/cellpose/__init__.py
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Expand Up @@ -4,13 +4,27 @@
from .download_checkpoint import download_checkpoint

models_dict = {
"jrc_fly-mb-z0419-20_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_fly-mb-z0419-20_nuc_cp",
"jrc_mus-epididymis-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-epididymis-1_nuc_cp",
"jrc_mus-epididymis-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-epididymis-2_nuc_cp",
"jrc_mus-granule-neurons-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-granule-neurons-1_nuc_cp",
"jrc_mus-granule-neurons-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-granule-neurons-2_nuc_cp",
"jrc_mus-granule-neurons-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-granule-neurons-3_nuc_cp",
"jrc_mus-guard-hair-follicle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-guard-hair-follicle_nuc_cp",
"jrc_mus-heart-1_ecs_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-heart-1_ecs_cp",
"jrc_mus-heart-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-heart-1_nuc_cp",
"jrc_mus-hippocampus-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-hippocampus-1_nuc_cp",
"jrc_mus-kidney_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-kidney_nuc_cp",
"jrc_mus-kidney-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-kidney-2_nuc_cp",
"jrc_mus-kidney-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney-3_nuc_cp",
"jrc_mus-liver-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-liver-2_nuc_cp",
"jrc_mus-liver-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-liver-3_nuc_cp",
"jrc_mus-meissner-corpuscle-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-meissner-corpuscle-1_nuc_cp",
"jrc_mus-meissner-corpuscle-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-meissner-corpuscle-2_nuc_cp",
"jrc_mus-pacinian-corpuscle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06jrc_mus-pacinian-corpuscle_nuc_cp",
"jrc_mus-pancreas-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-pancreas-1_nuc_cp",
"jrc_mus-pancreas-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-pancreas-2_nuc_cp",
"jrc_mus-pancreas-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-pancreas-3_nuc_cp",
"jrc_mus-pancreas-4_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas-4_nuc_cp",
"jrc_mus-skin-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-skin-1_nuc_cp",
"jrc_mus-thymus-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-thymus-1_nuc_cp",
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