napari-tmidas 0.2.0__tar.gz → 0.2.2__tar.gz

{napari_tmidas-0.2.0 → napari_tmidas-0.2.2}/.github/workflows/test_and_deploy.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v4

{napari_tmidas-0.2.0 → napari_tmidas-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.2.0
+Version: 0.2.2
 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
@@ -48,13 +48,13 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Image Processing
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: magicgui
+Requires-Dist: tqdm
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
 Requires-Dist: pyqt5
@@ -66,6 +66,14 @@ Requires-Dist: torch
 Requires-Dist: torchvision
 Requires-Dist: timm
 Requires-Dist: opencv-python
+Requires-Dist: cmake
+Requires-Dist: nd2
+Requires-Dist: pylibCZIrw
+Requires-Dist: readlif
+Requires-Dist: tiffslide
+Requires-Dist: hydra-core
+Requires-Dist: eva-decord
+Requires-Dist: acquifer-napari
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -90,9 +98,11 @@ Currently, napari-tmidas provides pipelines as widgets for batch image conversio
 
 ## Installation
 
+(Video installation guides: https://www.youtube.com/@macromeer/videos)
+
 First, install Napari in a virtual environment:
 
-    mamba create -y -n napari-tmidas -c conda-forge python=3.11 tqdm
+    mamba create -y -n napari-tmidas -c conda-forge python=3.11
     mamba activate napari-tmidas
     python -m pip install "napari[all]"
 
@@ -100,27 +110,28 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-It is recommended to install the latest development version:
+It is recommended though to install the **latest development version**. Please also execute this command from time to time in the activated environment to benefit from newly added features:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
-### Dependencies
-
-To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
+To use the Batch Crop Anything pipeline, we need to install **Segment Anything 2** (2D/3D):
 
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
+    cd /opt # if the folder does not exist: mkdir /opt && cd /opt
+    git clone https://github.com/facebookresearch/sam2.git && cd sam2
+    pip install -e .
+    curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
+    mamba install -c conda-forge ffmpeg # we also need ffmpeg
 
-For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
+If you want to batch compress image data using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
 
-    pip install git+https://github.com/ChaoningZhang/MobileSAM.git
+   ~~sudo apt-get install zstd~~    # Pre-installed on Linux :man_shrugging:
 
+    brew install zstd            # for macOS (requires [Homebrew](https://brew.sh/)
+    pip install zstandard        # Windows with Python >= 3.7
 
-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
 
+And you are done! 
 
 ## Usage
 
@@ -153,24 +164,33 @@ 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;">
 
 
 Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
 
+
+#### Processing Function Credits
+
+The image processing capabilities are powered by several excellent open-source tools:
+- [Cellpose 4](https://github.com/MouseLand/cellpose): Advanced cell segmentation
+- [Trackastra](https://github.com/weigertlab/trackastra): Cell tracking and analysis
+- [CAREamics](https://github.com/CAREamics/careamics): Content-aware image restoration and enhancement
+
 ### Batch Label Inspection
 If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the `Plugins > T-MIDAS > Batch Label Inspection`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
 
 <img src="https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e" alt="Batch Label Inspection Widget" style="width:75%; height:auto;">
 
-
 ### Crop Anything
-This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`. Click the image below to see a video demo.
+This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`. Cropping works like this: Enter 2D view and go to the first z slice where the object to be cropped is appearing. Activate/select the points layer and click on the object. Terminal shows progress. You can then proceed to select another object (always do this in 2D mode)
 
 <img src="https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443" alt="Crop Anything Widget" style="width:75%; height:auto;">
 
 
+
+
 ### ROI Colocalization
 This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.
 

{napari_tmidas-0.2.0 → napari_tmidas-0.2.2}/README.md

@@ -13,9 +13,11 @@ Currently, napari-tmidas provides pipelines as widgets for batch image conversio
 
 ## Installation
 
+(Video installation guides: https://www.youtube.com/@macromeer/videos)
+
 First, install Napari in a virtual environment:
 
-    mamba create -y -n napari-tmidas -c conda-forge python=3.11 tqdm
+    mamba create -y -n napari-tmidas -c conda-forge python=3.11
     mamba activate napari-tmidas
     python -m pip install "napari[all]"
 
@@ -23,27 +25,28 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-It is recommended to install the latest development version:
+It is recommended though to install the **latest development version**. Please also execute this command from time to time in the activated environment to benefit from newly added features:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
-### Dependencies
-
-To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
+To use the Batch Crop Anything pipeline, we need to install **Segment Anything 2** (2D/3D):
 
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
+    cd /opt # if the folder does not exist: mkdir /opt && cd /opt
+    git clone https://github.com/facebookresearch/sam2.git && cd sam2
+    pip install -e .
+    curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
+    mamba install -c conda-forge ffmpeg # we also need ffmpeg
 
-For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
+If you want to batch compress image data using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
 
-    pip install git+https://github.com/ChaoningZhang/MobileSAM.git
+   ~~sudo apt-get install zstd~~    # Pre-installed on Linux :man_shrugging:
 
+    brew install zstd            # for macOS (requires [Homebrew](https://brew.sh/)
+    pip install zstandard        # Windows with Python >= 3.7
 
-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
 
+And you are done! 
 
 ## Usage
 
@@ -76,24 +79,33 @@ 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;">
 
 
 Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
 
+
+#### Processing Function Credits
+
+The image processing capabilities are powered by several excellent open-source tools:
+- [Cellpose 4](https://github.com/MouseLand/cellpose): Advanced cell segmentation
+- [Trackastra](https://github.com/weigertlab/trackastra): Cell tracking and analysis
+- [CAREamics](https://github.com/CAREamics/careamics): Content-aware image restoration and enhancement
+
 ### Batch Label Inspection
 If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the `Plugins > T-MIDAS > Batch Label Inspection`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
 
 <img src="https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e" alt="Batch Label Inspection Widget" style="width:75%; height:auto;">
 
-
 ### Crop Anything
-This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`. Click the image below to see a video demo.
+This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`. Cropping works like this: Enter 2D view and go to the first z slice where the object to be cropped is appearing. Activate/select the points layer and click on the object. Terminal shows progress. You can then proceed to select another object (always do this in 2D mode)
 
 <img src="https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443" alt="Crop Anything Widget" style="width:75%; height:auto;">
 
 
+
+
 ### ROI Colocalization
 This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.
 

{napari_tmidas-0.2.0 → napari_tmidas-0.2.2}/pyproject.toml

@@ -20,13 +20,13 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
 requires-python = ">=3.9"
 dependencies = [
     "numpy",
     "magicgui",
+    "tqdm",
     "qtpy",
     "scikit-image",
     "pyqt5",
@@ -38,6 +38,14 @@ dependencies = [
     "torchvision",
     "timm",
     "opencv-python",
+    "cmake",
+    "nd2",
+    "pylibCZIrw",
+    "readlif",
+    "tiffslide",
+    "hydra-core",
+    "eva-decord",
+    "acquifer-napari",
 ]
 
 [project.optional-dependencies]