Merge pull request #7 from janelia-cellmap/aemmav-patch-1

Update README.md with more cellpose models

src/cellmap_models/pytorch/cellpose/README.md

@@ -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:

src/cellmap_models/pytorch/cellpose/__init__.py

@@ -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",