napari-tmidas 0.2.1__tar.gz → 0.2.4__tar.gz

{napari_tmidas-0.2.1 → napari_tmidas-0.2.4}/.github/workflows/test_and_deploy.yml

@@ -23,8 +23,8 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        platform: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v4
@@ -37,13 +37,6 @@ jobs:
       # these libraries enable testing on Qt on linux
       - uses: tlambert03/setup-qt-libs@v1
 
-      # strategy borrowed from vispy for installing opengl libs on windows
-      - name: Install Windows OpenGL
-        if: runner.os == 'Windows'
-        run: |
-          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
-          powershell gl-ci-helpers/appveyor/install_opengl.ps1
-
       # note: if you need dependencies from conda, considering using
       # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
       # and
@@ -53,13 +46,75 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install setuptools tox tox-gh-actions
 
+      - name: Pip cache
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml', 'tox.ini') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Remove .tox cache
+        run: rm -rf .tox
+
+      - name: Free up disk space (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          # Remove unnecessary tools and packages to free up disk space
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /usr/local/lib/android
+          sudo rm -rf /opt/ghc
+          sudo rm -rf /opt/hostedtoolcache/CodeQL
+          sudo docker image prune --all --force
+          df -h
+
+      - name: Upgrade critical dependencies
+        run: |
+          python -m pip install --upgrade numpy psygnal pytest
+          python -m pip install --upgrade pip setuptools wheel
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libgl1-mesa-dev \
+            libglib2.0-0 \
+            libsm6 \
+            libxext6 \
+            libxrender1 \
+            libgomp1
+
       # this runs the platform-specific tests declared in tox.ini
       - name: Test with tox
         uses: aganders3/headless-gui@v2
         with:
-          run: python -m tox
+          run: python -m tox -r -- -m "not slow"
         env:
           PLATFORM: ${{ matrix.platform }}
+          QT_QPA_PLATFORM: offscreen
+          MPLBACKEND: Agg
+          PYTHONUNBUFFERED: 1
+          PYTHONDONTWRITEBYTECODE: 1
+
+      - name: Show pytest summary (if available)
+        if: always()
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "Checking for coverage.xml..."
+          FOUND=0
+          if [ -f coverage.xml ]; then
+            echo "Found coverage.xml at repo root"; FOUND=1
+          fi
+          # Glob inside .tox envs (quiet if none)
+          if ls .tox/*/coverage.xml >/dev/null 2>&1; then
+            echo "Found coverage.xml inside .tox environment"; FOUND=1
+          fi
+          if [ "$FOUND" -eq 0 ]; then
+            echo "No coverage.xml found (this may be fine if tests were skipped).";
+            ls -al . | sed -n '1,120p'
+          fi
 
       - name: Coverage
         uses: codecov/codecov-action@v3

{napari_tmidas-0.2.1 → napari_tmidas-0.2.4}/.gitignore

@@ -82,3 +82,9 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
+
+# Test run artifacts (not source)
+slow_tests_output.txt
+tox_run_output.txt
+*_run_output.txt
+*tests_output.txt

{napari_tmidas-0.2.1 → napari_tmidas-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.2.1
+Version: 0.2.4
 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
@@ -41,38 +41,53 @@ Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Framework :: napari
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 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
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: numpy<2.0,>=1.23.0
 Requires-Dist: magicgui
+Requires-Dist: tqdm
 Requires-Dist: qtpy
-Requires-Dist: scikit-image
+Requires-Dist: scikit-image>=0.19.0
+Requires-Dist: scikit-learn-extra>=0.3.0
 Requires-Dist: pyqt5
-Requires-Dist: tqdm
-Requires-Dist: scikit-image
+Requires-Dist: zarr
 Requires-Dist: ome-zarr
 Requires-Dist: napari-ome-zarr
-Requires-Dist: torch
-Requires-Dist: torchvision
-Requires-Dist: timm
-Requires-Dist: opencv-python
+Requires-Dist: nd2
+Requires-Dist: pylibCZIrw
+Requires-Dist: readlif
+Requires-Dist: tiffslide
+Requires-Dist: acquifer-napari
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
-Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest>=7.0.0; extra == "testing"
 Requires-Dist: pytest-cov; extra == "testing"
 Requires-Dist: pytest-qt; extra == "testing"
+Requires-Dist: pytest-timeout; extra == "testing"
 Requires-Dist: napari; extra == "testing"
 Requires-Dist: pyqt5; extra == "testing"
+Requires-Dist: psygnal>=0.8.0; extra == "testing"
+Provides-Extra: clustering
+Requires-Dist: scikit-learn-extra>=0.3.0; extra == "clustering"
+Provides-Extra: deep-learning
+Requires-Dist: torch>=1.12.0; extra == "deep-learning"
+Requires-Dist: torchvision>=0.13.0; extra == "deep-learning"
+Requires-Dist: timm; extra == "deep-learning"
+Requires-Dist: opencv-python; extra == "deep-learning"
+Requires-Dist: cmake; extra == "deep-learning"
+Requires-Dist: hydra-core; extra == "deep-learning"
+Requires-Dist: eva-decord; extra == "deep-learning"
+Provides-Extra: all
+Requires-Dist: napari-tmidas[clustering,deep-learning,testing]; extra == "all"
 Dynamic: license-file
 
 # napari-tmidas
@@ -80,19 +95,21 @@ Dynamic: license-file
 [![License BSD-3](https://img.shields.io/pypi/l/napari-tmidas.svg?color=green)](https://github.com/macromeer/napari-tmidas/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
+[![Downloads](https://static.pepy.tech/badge/napari-tmidas)](https://pepy.tech/project/napari-tmidas)
 [![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) -->
-The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
+
+This napari plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the [T-MIDAS terminal](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
 ## Features
-Currently, napari-tmidas provides pipelines as widgets for batch image conversion / cropping / processing, ROI colocalization and label inspection (cf. [Usage](#usage) below).
+Currently, **napari-tmidas** provides pipelines as widgets for batch image conversion and processing, object cropping, label image inspection and ROI colocalization (cf. [usage](#usage) below). You can request new batch image processing features in [issues](https://github.com/MercaderLabAnatomy/napari-tmidas/issues).
 
 ## 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]"
 
@@ -100,34 +117,36 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-It is recommended to install the latest development version. Please also regularly execute this command in the activated environment:
+**For deep learning features** (Batch Crop Anything with SAM2, Spotiflow, Careamics, Trackastra), also install:
 
-    pip install git+https://github.com/macromeer/napari-tmidas.git
+    pip install 'napari-tmidas[deep-learning]'
 
-### Dependencies
+Or install everything at once:
 
-To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
+    pip install 'napari-tmidas[all]'
 
-    # mamba activate napari-tmidas
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
+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:
 
-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:
+    pip install git+https://github.com/MercaderLabAnatomy/napari-tmidas.git
 
-    sudo apt-get install zstd    # for Linux
-    brew install zstd            # for macOS
-    choco install zstandard      # for Windows
+### Additional Setup for Batch Crop Anything
 
-To use the Batch Crop Anything pipeline, we need to install SAM2 in the napari-tmidas environment:
+To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
 
-    # mamba activate napari-tmidas
-    cd /opt
+    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 .
-    wget https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -P checkpoints/
-    pip install decord
+    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
+
+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:
 
+   ~~sudo apt-get install zstd~~    # Pre-installed on Linux :man_shrugging:
 
+    brew install zstd            # for macOS (requires Homebrew)
+    pip install zstandard        # Windows with Python >= 3.7
 
+And you are done!
 
 ## Usage
 
@@ -139,19 +158,22 @@ You can then find the installed plugin in the Plugins tab.
 
 ### Microscopy Image Conversion
 
-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.
+Converts `.lif, .nd2, .czi, .ndpi` and Acquifer data to TIF or OME-Zarr formats. Scan a folder, select files, and export with preserved spatial metadata.
 
+**Supported Formats:**
+- **TIF** - Standard format for compatibility
+- **OME-Zarr** - Recommended for large datasets, [spec v0.5](https://ngff.openmicroscopy.org/latest/) compliant with automatic physical metadata extraction (voxel sizes, spacing)
 
 <img src="https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b" alt="Microscopy Image Conversion Widget" style="width:75%; height:auto;">
 
 
 ### Image Processing
 
-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.
+1. You start with entering the path to the folder containing the images to be processed (currently supports TIF, later also ZARR) and optionally a filter for filename suffix
 
 ![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
 
-2. As a result, a table appears with the found images. You can click on them to inspect them in the viewer.
+2. After indexing the files, a table appears with the found images. You can click on them to inspect them in the viewer.
 
 ![image](https://github.com/user-attachments/assets/8360942a-be8f-49ec-bc25-385ee43bd601)
 
@@ -166,19 +188,50 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 
 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
+- [VisCy](https://github.com/mehta-lab/VisCy): Virtual staining using deep learning
+- [CAREamics](https://github.com/CAREamics/careamics): Content-aware image restoration and enhancement
+- [Spotiflow](https://github.com/weigertlab/spotiflow): Accurate and efficient spot detection for fluorescence microscopy
+
+#### Processing Function Documentation
+
+Detailed documentation for specific processing functions:
+
+**Core Processing**
+- [Basic Processing Functions](docs/basic_processing.md) - Label and intensity operations, channel splitting/merging, time series
+- [Cellpose Segmentation](docs/cellpose_segmentation.md) - Deep learning cell/nucleus segmentation
+- [TrackAstra Tracking](docs/trackastra_tracking.md) - Cell tracking across time-lapse data
+- [VisCy Virtual Staining](docs/viscy_virtual_staining.md) - Virtual staining of phase/DIC images using deep learning
+
+**Analysis and Quality Control**
+- [Grid View: Intensity + Labels Overlay](docs/grid_view_overlay.md) - Visual QC for segmentation results
+- [Intensity-Based Label Filtering](docs/intensity_label_filter.md) - Filter labels by signal intensity
+- [Regionprops Analysis](docs/regionprops_analysis.md) - Extract quantitative properties from labels
+
+**Advanced Processing**
+- [Advanced Processing Functions](docs/advanced_processing.md) - Denoising (CAREamics), spot detection (Spotiflow), SciPy/scikit-image filters, compression, colocalization
+
 ### 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 (SAM2; supports YX, ZYX and TYX data) 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.
 
 <img src="https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7" alt="ROI Colocalization Widget" style="width:75%; height:auto;">

{napari_tmidas-0.2.1 → napari_tmidas-0.2.4}/README.md

@@ -3,19 +3,21 @@
 [![License BSD-3](https://img.shields.io/pypi/l/napari-tmidas.svg?color=green)](https://github.com/macromeer/napari-tmidas/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
+[![Downloads](https://static.pepy.tech/badge/napari-tmidas)](https://pepy.tech/project/napari-tmidas)
 [![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) -->
-The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
+
+This napari plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the [T-MIDAS terminal](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
 ## Features
-Currently, napari-tmidas provides pipelines as widgets for batch image conversion / cropping / processing, ROI colocalization and label inspection (cf. [Usage](#usage) below).
+Currently, **napari-tmidas** provides pipelines as widgets for batch image conversion and processing, object cropping, label image inspection and ROI colocalization (cf. [usage](#usage) below). You can request new batch image processing features in [issues](https://github.com/MercaderLabAnatomy/napari-tmidas/issues).
 
 ## 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]"
 
@@ -23,34 +25,36 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-It is recommended to install the latest development version. Please also regularly execute this command in the activated environment:
+**For deep learning features** (Batch Crop Anything with SAM2, Spotiflow, Careamics, Trackastra), also install:
 
-    pip install git+https://github.com/macromeer/napari-tmidas.git
+    pip install 'napari-tmidas[deep-learning]'
 
-### Dependencies
+Or install everything at once:
 
-To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
+    pip install 'napari-tmidas[all]'
 
-    # mamba activate napari-tmidas
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
+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:
 
-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:
+    pip install git+https://github.com/MercaderLabAnatomy/napari-tmidas.git
 
-    sudo apt-get install zstd    # for Linux
-    brew install zstd            # for macOS
-    choco install zstandard      # for Windows
+### Additional Setup for Batch Crop Anything
 
-To use the Batch Crop Anything pipeline, we need to install SAM2 in the napari-tmidas environment:
+To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
 
-    # mamba activate napari-tmidas
-    cd /opt
+    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 .
-    wget https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -P checkpoints/
-    pip install decord
+    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
 
+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:
 
+   ~~sudo apt-get install zstd~~    # Pre-installed on Linux :man_shrugging:
 
+    brew install zstd            # for macOS (requires Homebrew)
+    pip install zstandard        # Windows with Python >= 3.7
+
+And you are done!
 
 ## Usage
 
@@ -62,19 +66,22 @@ You can then find the installed plugin in the Plugins tab.
 
 ### Microscopy Image Conversion
 
-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.
+Converts `.lif, .nd2, .czi, .ndpi` and Acquifer data to TIF or OME-Zarr formats. Scan a folder, select files, and export with preserved spatial metadata.
 
+**Supported Formats:**
+- **TIF** - Standard format for compatibility
+- **OME-Zarr** - Recommended for large datasets, [spec v0.5](https://ngff.openmicroscopy.org/latest/) compliant with automatic physical metadata extraction (voxel sizes, spacing)
 
 <img src="https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b" alt="Microscopy Image Conversion Widget" style="width:75%; height:auto;">
 
 
 ### Image Processing
 
-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.
+1. You start with entering the path to the folder containing the images to be processed (currently supports TIF, later also ZARR) and optionally a filter for filename suffix
 
 ![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
 
-2. As a result, a table appears with the found images. You can click on them to inspect them in the viewer.
+2. After indexing the files, a table appears with the found images. You can click on them to inspect them in the viewer.
 
 ![image](https://github.com/user-attachments/assets/8360942a-be8f-49ec-bc25-385ee43bd601)
 
@@ -89,19 +96,50 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 
 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
+- [VisCy](https://github.com/mehta-lab/VisCy): Virtual staining using deep learning
+- [CAREamics](https://github.com/CAREamics/careamics): Content-aware image restoration and enhancement
+- [Spotiflow](https://github.com/weigertlab/spotiflow): Accurate and efficient spot detection for fluorescence microscopy
+
+#### Processing Function Documentation
+
+Detailed documentation for specific processing functions:
+
+**Core Processing**
+- [Basic Processing Functions](docs/basic_processing.md) - Label and intensity operations, channel splitting/merging, time series
+- [Cellpose Segmentation](docs/cellpose_segmentation.md) - Deep learning cell/nucleus segmentation
+- [TrackAstra Tracking](docs/trackastra_tracking.md) - Cell tracking across time-lapse data
+- [VisCy Virtual Staining](docs/viscy_virtual_staining.md) - Virtual staining of phase/DIC images using deep learning
+
+**Analysis and Quality Control**
+- [Grid View: Intensity + Labels Overlay](docs/grid_view_overlay.md) - Visual QC for segmentation results
+- [Intensity-Based Label Filtering](docs/intensity_label_filter.md) - Filter labels by signal intensity
+- [Regionprops Analysis](docs/regionprops_analysis.md) - Extract quantitative properties from labels
+
+**Advanced Processing**
+- [Advanced Processing Functions](docs/advanced_processing.md) - Denoising (CAREamics), spot detection (Spotiflow), SciPy/scikit-image filters, compression, colocalization
+
 ### 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 (SAM2; supports YX, ZYX and TYX data) 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.
 
 <img src="https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7" alt="ROI Colocalization Widget" style="width:75%; height:auto;">