Update Cellpose model URLs

janelia-cellmap · Mar 8, 2024 · 20381fc · 20381fc
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diff --git a/src/cellmap_models/pytorch/cellpose/README.md b/src/cellmap_models/pytorch/cellpose/README.md
@@ -6,16 +6,25 @@ This directory contains finetuned scripts for downloading Cellpose models, parti
 ## Models
 
 ### Trained on p7 mouse tissues
-- __CP_jrc_mus-thymus-1-nuc-2__: trained on thymus nuclei
-- __CP_jrc_mus-skin-1-nuc__:
-- __CP_jrc_mus-pancreas-4_nuc__:
-- __CP_jrc_mus-heart-1-nuc-2__:
-- __CP_jrc_mus-heart-1-ecs__:
-- __CP_jrc_mus-epididymis-1-nuc__:
-- __CP_jrc_mus-epididymis-2-nuc__:
-- __CP_jrc_mus-kidney-3-nuc-2__:
-- __CP_jrc_mus-liver-3-nuc-2__:
-- __CP_jrc_mus-hippocampus-1-nuc-2__:
+**jrc_mus-epididymis-1_nuc_cp:**
+
+**jrc_mus-epididymis-2_nuc_cp:**
+
+**jrc_mus-heart-1_ecs_cp:**
+
+**jrc_mus-heart-1_nuc_cp:**
+
+**jrc_mus-hippocampus-1_nuc_cp:**
+
+**jrc_mus-kidney-3_nuc_cp:**
+
+**jrc_mus-liver-3_nuc_cp:**
+
+**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:** 
 
 ## Usage
 
@@ -28,19 +37,27 @@ from cellmap_models.cellpose import load_model
 model = load_model('<model_name>')
 ```
 
+Where `<model_name>` is the name of the model you would like to download.
+
+```python
+
 __If you would like to download and use a Cellpose model with the `cellpose` package or its GUI, do so by following the instructions below.__
 
 First install the `cellpose` package:
 
 ```bash
 conda activate cellmap
-pip install cellpose[gui]
+pip install "cellpose[gui]"
 ```
 
-Then you can also download model weights from the `cellmap-models` repository and add them to your local `cellpose` model directory. For example, you can run the following commands:
+Then you can also download model weights from the `cellmap-models` repository and add them to your local Cellpose model directory. For example, you can run the following commands:
 
 ```bash
 cellmap.add_cellpose <model_name>
 ```
 
-where `<model_name>` is the name of the model you would like to download, based on the descriptions above. For example, to download the `...
+where `<model_name>` is the name of the model you would like to download, based on the descriptions above. For example, to download the `jrc_mus-pancreas-4_nuc_cp` model and add it to Cellpose, you would run:
+
+```bash
+cellmap.add_cellpose jrc_mus-pancreas-4_nuc_cp
+```
diff --git a/src/cellmap_models/pytorch/cellpose/__init__.py b/src/cellmap_models/pytorch/cellpose/__init__.py
@@ -2,16 +2,16 @@
 from .load_model import load_model
 
 models_dict = {
-    "CP_jrc_mus-thymus-1-nuc-2": "...",
-    "CP_jrc_mus-skin-1-nuc": "...",
-    "CP_jrc_mus-pancreas-4_nuc": "...",
-    "CP_jrc_mus-heart-1-nuc-2": "...",
-    "CP_jrc_mus-heart-1-ecs": "...",
-    "CP_jrc_mus-epididymis-1-nuc": "...",
-    "CP_jrc_mus-epididymis-2-nuc": "...",
-    "CP_jrc_mus-kidney-3-nuc-2": "...",
-    "CP_jrc_mus-liver-3-nuc-2": "...",
-    "CP_jrc_mus-hippocampus-1-nuc-2": "...",
+    "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-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-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney-3_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-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",
 }
 
 models_list = list(models_dict.keys())