napari-tmidas 0.2.0__tar.gz → 0.2.1__tar.gz

{napari_tmidas-0.2.0 → napari_tmidas-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.2.0
+Version: 0.2.1
 Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
 Author: Marco Meer
 Author-email: marco.meer@pm.me
@@ -100,7 +100,7 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-It is recommended to install the latest development version:
+It is recommended to install the latest development version. Please also regularly execute this command in the activated environment:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
@@ -108,19 +108,26 @@ It is recommended to install the latest development version:
 
 To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
 
+    # mamba activate napari-tmidas
     pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
 
-For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
-
-    pip install git+https://github.com/ChaoningZhang/MobileSAM.git
-
-
 If you want to batch compress images using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
 
     sudo apt-get install zstd    # for Linux
     brew install zstd            # for macOS
     choco install zstandard      # for Windows
 
+To use the Batch Crop Anything pipeline, we need to install SAM2 in the napari-tmidas environment:
+
+    # mamba activate napari-tmidas
+    cd /opt
+    git clone https://github.com/facebookresearch/sam2.git && cd sam2
+    pip install -e .
+    wget https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -P checkpoints/
+    pip install decord
+
+
+
 
 ## Usage
 
@@ -153,7 +160,7 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 ![image](https://github.com/user-attachments/assets/05929660-6672-4f76-89da-4f17749ccfad)
 
 4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
-   
+
 <img src="https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce" alt="Image Processing Widget" style="width:75%; height:auto;">
 
 

{napari_tmidas-0.2.0 → napari_tmidas-0.2.1}/README.md

@@ -23,7 +23,7 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-It is recommended to install the latest development version:
+It is recommended to install the latest development version. Please also regularly execute this command in the activated environment:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
@@ -31,19 +31,26 @@ It is recommended to install the latest development version:
 
 To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
 
+    # mamba activate napari-tmidas
     pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
 
-For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
-
-    pip install git+https://github.com/ChaoningZhang/MobileSAM.git
-
-
 If you want to batch compress images using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
 
     sudo apt-get install zstd    # for Linux
     brew install zstd            # for macOS
     choco install zstandard      # for Windows
 
+To use the Batch Crop Anything pipeline, we need to install SAM2 in the napari-tmidas environment:
+
+    # mamba activate napari-tmidas
+    cd /opt
+    git clone https://github.com/facebookresearch/sam2.git && cd sam2
+    pip install -e .
+    wget https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -P checkpoints/
+    pip install decord
+
+
+
 
 ## Usage
 
@@ -76,7 +83,7 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 ![image](https://github.com/user-attachments/assets/05929660-6672-4f76-89da-4f17749ccfad)
 
 4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
-   
+
 <img src="https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce" alt="Image Processing Widget" style="width:75%; height:auto;">