napari-tmidas 0.2.6__tar.gz → 0.3.1__tar.gz

{napari_tmidas-0.2.6 → napari_tmidas-0.3.1}/.github/workflows/test_and_deploy.yml

@@ -44,8 +44,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools tox tox-gh-actions
-
+          python -m pip install setuptools tox tox-gh-actions scikit-learn-extra
+          
       - name: Pip cache
         uses: actions/cache@v4
         with:

napari_tmidas-0.3.1/PKG-INFO

@@ -0,0 +1,246 @@
+Metadata-Version: 2.4
+Name: napari-tmidas
+Version: 0.3.1
+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
+License: 
+        Copyright (c) 2025, Marco Meer
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Bug Tracker, https://github.com/macromeer/napari-tmidas/issues
+Project-URL: Documentation, https://github.com/macromeer/napari-tmidas#README.md
+Project-URL: Source Code, https://github.com/macromeer/napari-tmidas
+Project-URL: User Support, https://github.com/macromeer/napari-tmidas/issues
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+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 :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<3.0,>=1.23.0
+Requires-Dist: magicgui
+Requires-Dist: tqdm
+Requires-Dist: qtpy
+Requires-Dist: scikit-image>=0.19.0
+Requires-Dist: scikit-learn-extra>=0.3.0
+Requires-Dist: pyqt5
+Requires-Dist: zarr
+Requires-Dist: ome-zarr
+Requires-Dist: napari-ome-zarr
+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>=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"
+Requires-Dist: scikit-learn-extra>=0.3.0; 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
+
+[![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)
+[![DOI](https://zenodo.org/badge/943353883.svg)](https://doi.org/10.5281/zenodo.17988815)
+[![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
+
+**AI-powered batch processing for microscopy images**
+
+Transform, analyze, and quantify microscopy data at scale with deep learning - from file conversion to segmentation, tracking, and analysis.
+
+## ✨ Key Features
+
+🤖 **5 AI Methods Built-In**
+- Virtual staining (VisCy) • Denoising (CAREamics) • Spot detection (Spotiflow) • Segmentation (Cellpose) • Tracking (Trackastra)
+- Auto-install in isolated environments • No dependency conflicts • GPU acceleration
+
+🔄 **Universal File Conversion**
+- Convert LIF, ND2, CZI, NDPI, Acquifer → TIFF or OME-Zarr
+- Preserve spatial metadata automatically
+
+⚡ **Batch Processing**
+- Process entire folders with one click • 40+ processing functions • Progress tracking & quality control
+
+📊 **Complete Analysis Pipeline**
+- Segmentation → Tracking → Quantification → Colocalization
+
+## 🚀 Quick Start
+
+```bash
+# Install napari and the plugin
+mamba create -y -n napari-tmidas -c conda-forge python=3.11
+mamba activate napari-tmidas
+pip install "napari[all]"
+pip install napari-tmidas
+
+# Launch napari
+napari
+```
+
+Then find napari-tmidas in the **Plugins** menu. [Watch video tutorials →](https://www.youtube.com/@macromeer/videos)
+
+> **💡 Tip**: AI methods auto-install their dependencies on first use - no manual setup required!
+
+## 📖 Documentation
+
+### AI-Powered Methods
+
+| Method | Description | Documentation |
+|--------|-------------|---------------|
+| 🎨 **VisCy** | Virtual staining from phase/DIC | [Guide](docs/viscy_virtual_staining.md) |
+| 🔧 **CAREamics** | Noise2Void/CARE denoising | [Guide](docs/careamics_denoising.md) |
+| 🎯 **Spotiflow** | Spot/puncta detection | [Guide](docs/spotiflow_detection.md) |
+| 🔬 **Cellpose** | Cell/nucleus segmentation | [Guide](docs/cellpose_segmentation.md) |
+| 📈 **Trackastra** | Cell tracking over time | [Guide](docs/trackastra_tracking.md) |
+
+### Core Workflows
+
+- **[File Conversion](docs/file_conversion.md)** - Multi-format microscopy file conversion (LIF, ND2, CZI, NDPI, Acquifer)
+- **[Batch Processing](docs/basic_processing.md)** - Label operations, filters, channel splitting
+- **[Quality Control](docs/grid_view_overlay.md)** - Visual QC with grid overlay
+- **[Quantification](docs/regionprops_analysis.md)** - Extract measurements from labels
+- **[Colocalization](docs/advanced_processing.md#colocalization-analysis)** - Multi-channel ROI analysis
+
+### Advanced Features
+
+- [SAM2 Crop Anything](docs/advanced_processing.md#sam2) - Interactive object cropping
+- [Advanced Filters](docs/advanced_processing.md) - SciPy/scikit-image filters
+- [Batch Label Inspection](docs/basic_processing.md#label-inspection) - Manual correction workflow
+
+## 💻 Installation
+
+### Step 1: Install napari
+
+```bash
+mamba create -y -n napari-tmidas -c conda-forge python=3.11
+mamba activate napari-tmidas
+python -m pip install "napari[all]"
+```
+
+### Step 2: Install napari-tmidas
+
+| Your Needs | Command |
+|----------|---------|
+| **Just process & convert images** | `pip install napari-tmidas` |
+| **Need AI features** (SAM2, Cellpose, Spotiflow, etc.) | `pip install 'napari-tmidas[deep-learning]'` |
+| **Want the latest dev features** | `pip install git+https://github.com/MercaderLabAnatomy/napari-tmidas.git` |
+
+**Recommended for most users:** `pip install 'napari-tmidas[deep-learning]'`
+
+## 🖼️ Screenshots
+
+<details>
+<summary><b>File Conversion Widget</b></summary>
+
+<img src="https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b" alt="File Conversion" width="600">
+
+Convert proprietary formats to open standards with metadata preservation.
+</details>
+
+<details>
+<summary><b>Batch Processing Interface</b></summary>
+
+<img src="https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce" alt="Batch Processing" width="600">
+
+Select files → Choose processing function → Run on entire dataset.
+</details>
+
+<details>
+<summary><b>Label Inspection</b></summary>
+
+<img src="https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e" alt="Label Inspection" width="600">
+
+Inspect and manually correct segmentation results.
+</details>
+
+<details>
+<summary><b>SAM2 Crop Anything</b></summary>
+
+<img src="https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443" alt="Crop Anything" width="600">
+
+Interactive object selection and cropping with SAM2.
+</details>
+
+## 🤝 Contributing
+
+Contributions are welcome! Please ensure tests pass before submitting PRs:
+
+```bash
+pip install tox
+tox
+```
+
+## 📄 License
+
+BSD-3 License - see [LICENSE](LICENSE) for details.
+
+## 🐛 Issues
+
+Found a bug or have a feature request? [Open an issue](https://github.com/MercaderLabAnatomy/napari-tmidas/issues)
+
+## 🙏 Acknowledgments
+
+Built with [napari](https://github.com/napari/napari) and powered by:
+- [Cellpose](https://github.com/MouseLand/cellpose) • [VisCy](https://github.com/mehta-lab/VisCy) • [CAREamics](https://github.com/CAREamics/careamics) • [Spotiflow](https://github.com/weigertlab/spotiflow) • [Trackastra](https://github.com/weigertlab/trackastra) • [SAM2](https://github.com/facebookresearch/segment-anything-2)
+
+---
+
+[PyPI]: https://pypi.org/project/napari-tmidas
+[pip]: https://pypi.org/project/pip/
+[tox]: https://tox.readthedocs.io/en/latest/

napari_tmidas-0.3.1/README.md

@@ -0,0 +1,153 @@
+# napari-tmidas
+
+[![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)
+[![DOI](https://zenodo.org/badge/943353883.svg)](https://doi.org/10.5281/zenodo.17988815)
+[![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
+
+**AI-powered batch processing for microscopy images**
+
+Transform, analyze, and quantify microscopy data at scale with deep learning - from file conversion to segmentation, tracking, and analysis.
+
+## ✨ Key Features
+
+🤖 **5 AI Methods Built-In**
+- Virtual staining (VisCy) • Denoising (CAREamics) • Spot detection (Spotiflow) • Segmentation (Cellpose) • Tracking (Trackastra)
+- Auto-install in isolated environments • No dependency conflicts • GPU acceleration
+
+🔄 **Universal File Conversion**
+- Convert LIF, ND2, CZI, NDPI, Acquifer → TIFF or OME-Zarr
+- Preserve spatial metadata automatically
+
+⚡ **Batch Processing**
+- Process entire folders with one click • 40+ processing functions • Progress tracking & quality control
+
+📊 **Complete Analysis Pipeline**
+- Segmentation → Tracking → Quantification → Colocalization
+
+## 🚀 Quick Start
+
+```bash
+# Install napari and the plugin
+mamba create -y -n napari-tmidas -c conda-forge python=3.11
+mamba activate napari-tmidas
+pip install "napari[all]"
+pip install napari-tmidas
+
+# Launch napari
+napari
+```
+
+Then find napari-tmidas in the **Plugins** menu. [Watch video tutorials →](https://www.youtube.com/@macromeer/videos)
+
+> **💡 Tip**: AI methods auto-install their dependencies on first use - no manual setup required!
+
+## 📖 Documentation
+
+### AI-Powered Methods
+
+| Method | Description | Documentation |
+|--------|-------------|---------------|
+| 🎨 **VisCy** | Virtual staining from phase/DIC | [Guide](docs/viscy_virtual_staining.md) |
+| 🔧 **CAREamics** | Noise2Void/CARE denoising | [Guide](docs/careamics_denoising.md) |
+| 🎯 **Spotiflow** | Spot/puncta detection | [Guide](docs/spotiflow_detection.md) |
+| 🔬 **Cellpose** | Cell/nucleus segmentation | [Guide](docs/cellpose_segmentation.md) |
+| 📈 **Trackastra** | Cell tracking over time | [Guide](docs/trackastra_tracking.md) |
+
+### Core Workflows
+
+- **[File Conversion](docs/file_conversion.md)** - Multi-format microscopy file conversion (LIF, ND2, CZI, NDPI, Acquifer)
+- **[Batch Processing](docs/basic_processing.md)** - Label operations, filters, channel splitting
+- **[Quality Control](docs/grid_view_overlay.md)** - Visual QC with grid overlay
+- **[Quantification](docs/regionprops_analysis.md)** - Extract measurements from labels
+- **[Colocalization](docs/advanced_processing.md#colocalization-analysis)** - Multi-channel ROI analysis
+
+### Advanced Features
+
+- [SAM2 Crop Anything](docs/advanced_processing.md#sam2) - Interactive object cropping
+- [Advanced Filters](docs/advanced_processing.md) - SciPy/scikit-image filters
+- [Batch Label Inspection](docs/basic_processing.md#label-inspection) - Manual correction workflow
+
+## 💻 Installation
+
+### Step 1: Install napari
+
+```bash
+mamba create -y -n napari-tmidas -c conda-forge python=3.11
+mamba activate napari-tmidas
+python -m pip install "napari[all]"
+```
+
+### Step 2: Install napari-tmidas
+
+| Your Needs | Command |
+|----------|---------|
+| **Just process & convert images** | `pip install napari-tmidas` |
+| **Need AI features** (SAM2, Cellpose, Spotiflow, etc.) | `pip install 'napari-tmidas[deep-learning]'` |
+| **Want the latest dev features** | `pip install git+https://github.com/MercaderLabAnatomy/napari-tmidas.git` |
+
+**Recommended for most users:** `pip install 'napari-tmidas[deep-learning]'`
+
+## 🖼️ Screenshots
+
+<details>
+<summary><b>File Conversion Widget</b></summary>
+
+<img src="https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b" alt="File Conversion" width="600">
+
+Convert proprietary formats to open standards with metadata preservation.
+</details>
+
+<details>
+<summary><b>Batch Processing Interface</b></summary>
+
+<img src="https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce" alt="Batch Processing" width="600">
+
+Select files → Choose processing function → Run on entire dataset.
+</details>
+
+<details>
+<summary><b>Label Inspection</b></summary>
+
+<img src="https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e" alt="Label Inspection" width="600">
+
+Inspect and manually correct segmentation results.
+</details>
+
+<details>
+<summary><b>SAM2 Crop Anything</b></summary>
+
+<img src="https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443" alt="Crop Anything" width="600">
+
+Interactive object selection and cropping with SAM2.
+</details>
+
+## 🤝 Contributing
+
+Contributions are welcome! Please ensure tests pass before submitting PRs:
+
+```bash
+pip install tox
+tox
+```
+
+## 📄 License
+
+BSD-3 License - see [LICENSE](LICENSE) for details.
+
+## 🐛 Issues
+
+Found a bug or have a feature request? [Open an issue](https://github.com/MercaderLabAnatomy/napari-tmidas/issues)
+
+## 🙏 Acknowledgments
+
+Built with [napari](https://github.com/napari/napari) and powered by:
+- [Cellpose](https://github.com/MouseLand/cellpose) • [VisCy](https://github.com/mehta-lab/VisCy) • [CAREamics](https://github.com/CAREamics/careamics) • [Spotiflow](https://github.com/weigertlab/spotiflow) • [Trackastra](https://github.com/weigertlab/trackastra) • [SAM2](https://github.com/facebookresearch/segment-anything-2)
+
+---
+
+[PyPI]: https://pypi.org/project/napari-tmidas
+[pip]: https://pypi.org/project/pip/
+[tox]: https://tox.readthedocs.io/en/latest/

{napari_tmidas-0.2.6 → napari_tmidas-0.3.1}/docs/advanced_processing.md

@@ -14,18 +14,13 @@ Image denoising using **CAREamics** (Content-Aware Image Restoration). This proc
 
 ## Installation
 
-CAREamics can be installed in your environment or will use a dedicated environment automatically.
-
-### Manual Installation (Recommended)
+CAREamics is automatically available when you install napari-tmidas with deep learning support:
 
 ```bash
-mamba activate napari-tmidas
-pip install careamics
+pip install 'napari-tmidas[deep-learning]'
 ```
 
-### Automatic Installation
-
-If not detected, the plugin creates a dedicated `careamics-env` conda environment automatically.
+If you installed the basic version without deep learning, the plugin will automatically create a dedicated `careamics-env` environment when first used.
 
 ## Parameters
 
@@ -116,16 +111,13 @@ Accurate spot detection for fluorescence microscopy using **Spotiflow**, a deep
 
 ## Installation
 
-### Manual Installation (Recommended)
+Spotiflow is automatically available when you install napari-tmidas with deep learning support:
 
 ```bash
-mamba activate napari-tmidas
-pip install spotiflow
+pip install 'napari-tmidas[deep-learning]'
 ```
 
-### Automatic Installation
-
-The plugin automatically creates a `spotiflow-env` conda environment if needed.
+If you installed the basic version without deep learning, the plugin will automatically create a `spotiflow-env` environment when first used.
 
 ## Pre-trained Models