From ce911ba8c1e494bf579b865da3d7bbe7c9b77610 Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Mon, 18 Mar 2024 13:37:32 -0400
Subject: [PATCH 1/2] fix typo

---
 src/cellmap_models/pytorch/cellpose/download_checkpoint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cellmap_models/pytorch/cellpose/download_checkpoint.py b/src/cellmap_models/pytorch/cellpose/download_checkpoint.py
index ea406bd..e68d4da 100755
--- a/src/cellmap_models/pytorch/cellpose/download_checkpoint.py
+++ b/src/cellmap_models/pytorch/cellpose/download_checkpoint.py
@@ -4,7 +4,7 @@
 
 def download_checkpoint(checkpoint_name: str, checkpoint_path: Path):
     """
-    download models checkpoint from s3 bucket.
+    download models checkpoint from github release.
 
     Args:
         checkpoint_name (str): Name of the checkpoint file.

From 895070395600cf2fb82cbbf94069055a5aa86642 Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Tue, 19 Mar 2024 14:56:48 -0400
Subject: [PATCH 2/2] add classes_channels to cosem models

---
 .../pytorch/cosem/setup04/model.py               | 16 ++++++++++++++++
 .../pytorch/cosem/setup26_1/model.py             |  1 +
 .../pytorch/cosem/setup28/model.py               |  1 +
 .../pytorch/cosem/setup36/model.py               |  1 +
 .../pytorch/cosem/setup45/model.py               |  1 +
 5 files changed, 20 insertions(+)

diff --git a/src/cellmap_models/pytorch/cosem/setup04/model.py b/src/cellmap_models/pytorch/cosem/setup04/model.py
index 437f85f..613e0f5 100755
--- a/src/cellmap_models/pytorch/cosem/setup04/model.py
+++ b/src/cellmap_models/pytorch/cosem/setup04/model.py
@@ -24,3 +24,19 @@
 final_feature_width = 12 * 6
 
 classes_out = 14
+classes_channels = [
+    "ecs",
+    "pm",
+    "mito",
+    "mito_mem",
+    "ves",
+    "ves_mem",
+    "endo",
+    "endo_mem",
+    "er",
+    "er_mem",
+    "eres",
+    "nuc",
+    "mt",
+    "mt_out",
+]
diff --git a/src/cellmap_models/pytorch/cosem/setup26_1/model.py b/src/cellmap_models/pytorch/cosem/setup26_1/model.py
index bc9916e..f13ce4a 100755
--- a/src/cellmap_models/pytorch/cosem/setup26_1/model.py
+++ b/src/cellmap_models/pytorch/cosem/setup26_1/model.py
@@ -24,3 +24,4 @@
 final_feature_width = 12 * 6
 
 classes_out = 3
+classes_channels = ["mito", "mito_mem", "mito_ribo"]
diff --git a/src/cellmap_models/pytorch/cosem/setup28/model.py b/src/cellmap_models/pytorch/cosem/setup28/model.py
index a3d4e36..2689c3d 100755
--- a/src/cellmap_models/pytorch/cosem/setup28/model.py
+++ b/src/cellmap_models/pytorch/cosem/setup28/model.py
@@ -24,3 +24,4 @@
 final_feature_width = 12 * 6
 
 classes_out = 2
+classes_channels = ["er", "er_mem"]
diff --git a/src/cellmap_models/pytorch/cosem/setup36/model.py b/src/cellmap_models/pytorch/cosem/setup36/model.py
index a3d4e36..2abfad9 100755
--- a/src/cellmap_models/pytorch/cosem/setup36/model.py
+++ b/src/cellmap_models/pytorch/cosem/setup36/model.py
@@ -24,3 +24,4 @@
 final_feature_width = 12 * 6
 
 classes_out = 2
+classes_channels = ["nuc", "nucleo"]
diff --git a/src/cellmap_models/pytorch/cosem/setup45/model.py b/src/cellmap_models/pytorch/cosem/setup45/model.py
index 938344e..2b4d995 100755
--- a/src/cellmap_models/pytorch/cosem/setup45/model.py
+++ b/src/cellmap_models/pytorch/cosem/setup45/model.py
@@ -24,3 +24,4 @@
 final_feature_width = 12 * 6
 
 classes_out = 2
+classes_channels = ["ecs", "pm"]