napari-tmidas 0.1.6__tar.gz → 0.1.7.1__tar.gz

{napari_tmidas-0.1.6 → napari_tmidas-0.1.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.1.6
+Version: 0.1.7.1
 Summary: Tissue Microscopy Image Data Analysis Suite
 Author: Marco Meer
 Author-email: marco.meer@pm.me
@@ -75,11 +75,30 @@ Dynamic: license-file
 [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-tmidas)](https://napari-hub.org/plugins/napari-tmidas)
 <!-- [![codecov](https://codecov.io/gh/macromeer/napari-tmidas/branch/main/graph/badge.svg)](https://codecov.io/gh/macromeer/napari-tmidas) -->
-This Napari plugin allows you to perform batch image processing without a graphics processing unit (GPU). It will still be fast because computations will run in parallel on your central processing unit (CPU).
+The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of microscopy images. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
-This plugin provides you with a growing collection of pipelines for batch image preprocessing, segmentation, regions-of-interest (ROI) analysis and other useful features.
+## Feature Overview
+
+1. **Image Processing**
+   - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
+
+2. **Label Inspection**
+   - Review and edit label images with auto-save
+
+3. **Microscopy Image Conversion**
+   - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
+
+4. **Crop Anything**
+   - Interactive ROI selection via click interface
+
+5. **ROI Colocalization**
+   - Count colocalized labels across multiple channels
+
+
+
+### Coming Soon
+New features arriving April 2025
 
-`napari-tmidas` is a work in progress (WIP) and an evolutionary step away from the [terminal / command-line version of T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
 ## Installation
 
@@ -98,29 +117,35 @@ To install the latest development version:
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
 ### Dependencies
-For the File converter, we need some libraries to read some microscopy formats and to write ome-zarr:
+To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats and to write ome-zarr:
 
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr
+    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr napari-ome-zarr
 
+For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
+
+    pip install git+https://github.com/ChaoningZhang/MobileSAM.git
+    pip install torch torchvision timm opencv-python
 
 ## Usage
 
+To use the plugin, start napari in the activated virtual environment with this terminal command:
+
+    mamba run -n napari-tmidas napari
+
 You can find the installed plugin here:
 
 ![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
 
 
-### File converter
+### Microscopy Image Conversion
 
-You might first want to batch convert microscopy image data. Currently, this plugin supports `.nd2, .lif, .ndpi, .czi` and acquifer data. After launching the file converter, you can scan a folder of your choice for microscopy image data. It will also detect series images that you can preview. Start by selecting an original image in the first column of the table. This allows you to preview or convert.
+You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
 
 ![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
 
+### Image Processing
 
-
-### File inspector
-
-1. After opening `Plugins > T-MIDAS > File selector`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
+1. After opening `Plugins > T-MIDAS > Batch Image Processing`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
 
 ![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
 
@@ -138,11 +163,20 @@ You might first want to batch convert microscopy image data. Currently, this plu
 
 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.
 
-### Label inspector
-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 > Label inspector`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
+### 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).
 
 ![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
 
+### 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`
+
+![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
+
+### 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_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
 
 
 ## Contributing

{napari_tmidas-0.1.6 → napari_tmidas-0.1.7.1}/README.md

@@ -6,11 +6,30 @@
 [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-tmidas)](https://napari-hub.org/plugins/napari-tmidas)
 <!-- [![codecov](https://codecov.io/gh/macromeer/napari-tmidas/branch/main/graph/badge.svg)](https://codecov.io/gh/macromeer/napari-tmidas) -->
-This Napari plugin allows you to perform batch image processing without a graphics processing unit (GPU). It will still be fast because computations will run in parallel on your central processing unit (CPU).
+The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of microscopy images. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
-This plugin provides you with a growing collection of pipelines for batch image preprocessing, segmentation, regions-of-interest (ROI) analysis and other useful features.
+## Feature Overview
+
+1. **Image Processing**
+   - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
+
+2. **Label Inspection**
+   - Review and edit label images with auto-save
+
+3. **Microscopy Image Conversion**
+   - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
+
+4. **Crop Anything**
+   - Interactive ROI selection via click interface
+
+5. **ROI Colocalization**
+   - Count colocalized labels across multiple channels
+
+
+
+### Coming Soon
+New features arriving April 2025
 
-`napari-tmidas` is a work in progress (WIP) and an evolutionary step away from the [terminal / command-line version of T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
 ## Installation
 
@@ -29,29 +48,35 @@ To install the latest development version:
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
 ### Dependencies
-For the File converter, we need some libraries to read some microscopy formats and to write ome-zarr:
+To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats and to write ome-zarr:
 
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr
+    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr napari-ome-zarr
 
+For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
+
+    pip install git+https://github.com/ChaoningZhang/MobileSAM.git
+    pip install torch torchvision timm opencv-python
 
 ## Usage
 
+To use the plugin, start napari in the activated virtual environment with this terminal command:
+
+    mamba run -n napari-tmidas napari
+
 You can find the installed plugin here:
 
 ![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
 
 
-### File converter
+### Microscopy Image Conversion
 
-You might first want to batch convert microscopy image data. Currently, this plugin supports `.nd2, .lif, .ndpi, .czi` and acquifer data. After launching the file converter, you can scan a folder of your choice for microscopy image data. It will also detect series images that you can preview. Start by selecting an original image in the first column of the table. This allows you to preview or convert.
+You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
 
 ![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
 
+### Image Processing
 
-
-### File inspector
-
-1. After opening `Plugins > T-MIDAS > File selector`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
+1. After opening `Plugins > T-MIDAS > Batch Image Processing`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
 
 ![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
 
@@ -69,11 +94,20 @@ You might first want to batch convert microscopy image data. Currently, this plu
 
 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.
 
-### Label inspector
-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 > Label inspector`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
+### 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).
 
 ![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
 
+### 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`
+
+![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
+
+### 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_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
 
 
 ## Contributing

{napari_tmidas-0.1.6 → napari_tmidas-0.1.7.1}/src/napari_tmidas/__init__.py

@@ -6,6 +6,7 @@ except ImportError:
 
 from ._label_inspection import label_inspector_widget
 from ._reader import napari_get_reader
+from ._roi_colocalization import roi_colocalization_analyzer
 from ._sample_data import make_sample_data
 from ._writer import write_multiple, write_single_image
 
@@ -16,4 +17,6 @@ __all__ = (
     "make_sample_data",
     "file_selector",
     "label_inspector_widget",
+    "batch_crop_anything_widget",
+    "roi_colocalization_analyzer",
 )