senoquant 1.0.0b1__py3-none-any.whl

senoquant-1.0.0b1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: senoquant
+Version: 1.0.0b1
+Summary: Napari plugin for spatial quantification of senescence markers in tissue imaging
+Author: SenoQuant Contributors
+Maintainer: SenoQuant Contributors
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/HaamsRee/senoquant-dev
+Project-URL: Documentation, https://haamsree.github.io/senoquant-dev/
+Project-URL: Repository, https://github.com/HaamsRee/senoquant-dev
+Project-URL: Bug Tracker, https://github.com/HaamsRee/senoquant-dev/issues
+Keywords: napari,plugin,senescence,quantification,microscopy,image analysis,segmentation,spot detection
+Classifier: Development Status :: 4 - Beta
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: bioio>=3.2.0
+Requires-Dist: bioio-czi>=2.4.2
+Requires-Dist: bioio-dv>=1.2.0
+Requires-Dist: bioio-imageio>=1.3.0
+Requires-Dist: bioio-lif>=1.4.0
+Requires-Dist: bioio-nd2>=1.6.0
+Requires-Dist: bioio-ome-tiff>=1.4.0
+Requires-Dist: bioio-ome-zarr>=3.2.1
+Requires-Dist: bioio-sldy>=1.4.0
+Requires-Dist: bioio-tifffile>=1.3.0
+Requires-Dist: bioio-tiff-glob>=1.2.0
+Requires-Dist: numpy<=1.26.4,>=1.23
+Requires-Dist: cellpose==4.0.8
+Requires-Dist: onnx>=1.16
+Requires-Dist: onnxruntime>=1.16; platform_system == "Darwin"
+Requires-Dist: onnxruntime-gpu>=1.16; platform_system != "Darwin"
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: huggingface_hub>=0.23.0
+Requires-Dist: scikit-image<0.25,>=0.22
+Requires-Dist: scipy>=1.8
+Requires-Dist: senoquant-stardist-ext>=0.1.0
+Requires-Dist: dask[array]>=2024.4
+Requires-Dist: dask[distributed]>=2024.4
+Provides-Extra: gpu
+Requires-Dist: cupy-cuda12x>=12.0; extra == "gpu"
+Requires-Dist: cucim>=23.4; extra == "gpu"
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Requires-Dist: bioio>=3.2.0; extra == "all"
+Requires-Dist: bioio-czi>=2.4.2; extra == "all"
+Requires-Dist: bioio-dv>=1.2.0; extra == "all"
+Requires-Dist: bioio-imageio>=1.3.0; extra == "all"
+Requires-Dist: bioio-lif>=1.4.0; extra == "all"
+Requires-Dist: bioio-nd2>=1.6.0; extra == "all"
+Requires-Dist: bioio-ome-tiff>=1.4.0; extra == "all"
+Requires-Dist: bioio-ome-zarr>=3.2.1; extra == "all"
+Requires-Dist: bioio-sldy>=1.4.0; extra == "all"
+Requires-Dist: bioio-tifffile>=1.3.0; extra == "all"
+Requires-Dist: bioio-tiff-glob>=1.2.0; extra == "all"
+Requires-Dist: numpy<=1.26.4,>=1.23; extra == "all"
+Requires-Dist: cellpose==4.0.8; extra == "all"
+Requires-Dist: onnx>=1.16; extra == "all"
+Requires-Dist: onnxruntime>=1.16; platform_system == "Darwin" and extra == "all"
+Requires-Dist: onnxruntime-gpu>=1.16; platform_system != "Darwin" and extra == "all"
+Requires-Dist: openpyxl>=3.1; extra == "all"
+Requires-Dist: huggingface_hub>=0.23.0; extra == "all"
+Requires-Dist: scikit-image<0.25,>=0.22; extra == "all"
+Requires-Dist: scipy>=1.8; extra == "all"
+Requires-Dist: senoquant-stardist-ext>=0.1.0; extra == "all"
+Requires-Dist: dask[array]>=2024.4; extra == "all"
+Requires-Dist: dask[distributed]>=2024.4; extra == "all"
+Requires-Dist: cupy-cuda12x>=12.0; extra == "all"
+Requires-Dist: cucim>=23.4; extra == "all"
+Dynamic: license-file
+
+# SenoQuant
+
+![tests](https://github.com/HaamsRee/senoquant-dev/actions/workflows/tests.yml/badge.svg)
+[![PyPI version](https://badge.fury.io/py/senoquant.svg)](https://badge.fury.io/py/senoquant)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+
+SenoQuant is a versatile Napari plugin designed for comprehensive, accurate,
+and unbiased spatial quantification and prediction of senescence markers
+across diverse tissue contexts.
+
+## Features
+
+- **Multi-Model Segmentation**: Nuclear and cytoplasmic segmentation with 5 built-in models
+  - StarDist ONNX (2D/3D)
+  - Cellpose SAM
+  - Morphological operations (dilation, perinuclear rings)
+- **Spot Detection**: Detect and quantify punctate senescence markers
+  - Undecimated B3-spline wavelet (UDWT)
+  - Rotational morphological processing (RMP)
+- **Quantification**: Extract intensity, morphology, and spot metrics
+  - Per-cell marker intensities
+  - Morphological descriptors
+  - Spot counting and colocalization
+- **Batch Processing**: Automated analysis of entire image folders
+  - Profile save/load for reproducibility
+  - Multi-scene file support
+- **File Format Support**: Microscopy formats via BioIO
+  - OME-TIFF, ND2, LIF, CZI, Zarr, and more
+
+## Installation
+
+### Prerequisites
+
+SenoQuant requires Python 3.11+ and napari:
+
+```bash
+conda create -n senoquant python=3.11
+conda activate senoquant
+pip install "napari[all]"
+```
+
+Or using `uv` (faster installer):
+
+```bash
+conda create -n senoquant python=3.11
+conda activate senoquant
+pip install uv
+uv pip install "napari[all]"
+```
+
+### Install SenoQuant
+
+```bash
+pip install senoquant
+```
+
+Or with `uv`:
+
+```bash
+uv pip install senoquant
+```
+
+Model files are downloaded automatically on first use from Hugging Face.
+To override the model repository, set `SENOQUANT_MODEL_REPO` environment variable.
+
+For GPU acceleration (Windows/Linux with CUDA):
+
+```bash
+pip install senoquant[gpu]
+```
+
+**Note:** The first launch of napari and the SenoQuant plugin will be slower as napari initializes and SenoQuant downloads model files (~1.3 GB) from Hugging Face. Subsequent launches will be faster as models are cached locally.
+
+## Quick Start
+
+1. **Launch napari and open your image:**
+   ```bash
+   napari
+   ```
+   File → Open File(s)... → Select your image
+
+2. **Open SenoQuant plugin:**  
+   Plugins → SenoQuant
+
+3. **Run segmentation:**  
+   Segmentation tab → Select nuclear channel → Choose model → Run
+
+4. **Detect spots (optional):**  
+   Spots tab → Select channel → Choose detector → Run
+
+5. **Export quantification:**  
+   Quantification tab → Configure features → Export
+
+6. **Batch process (optional):**  
+   Batch tab → Configure settings → Run Batch
+
+## Documentation
+
+Full documentation is available at [https://haamsree.github.io/senoquant-dev/](https://haamsree.github.io/senoquant-dev/)
+
+- [Installation Guide](https://haamsree.github.io/senoquant-dev/user/installation/)
+- [Quick Start Tutorial](https://haamsree.github.io/senoquant-dev/user/quickstart/)
+- [Segmentation Models](https://haamsree.github.io/senoquant-dev/user/segmentation/)
+- [Spot Detection](https://haamsree.github.io/senoquant-dev/user/spots/)
+- [Quantification Features](https://haamsree.github.io/senoquant-dev/user/quantification/)
+- [Batch Processing](https://haamsree.github.io/senoquant-dev/user/batch/)
+- [API Reference](https://haamsree.github.io/senoquant-dev/api/)
+
+## Development
+
+See the [Contributing Guide](https://haamsree.github.io/senoquant-dev/developer/contributing/) for development setup instructions.
+

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senoquant-1.0.0b1.dist-info/licenses/LICENSE

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+
+Copyright (c) 2026, SenoQuant Contributors
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. 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.
+
+3. Neither the name of the 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.

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