Metadata-Version: 2.4
Name: neutrophils-classifier-app
Version: 1.0.1
Summary: A GUI application for neutrophil classification using deep learning models
Author-email: Jacky Ka Long Ko <ka.ko@kennedy.ox.ac.uk>
License: MIT
Project-URL: Homepage, https://github.com/bpi-oxford/Neutrophils-Classifier-App
Project-URL: Repository, https://github.com/bpi-oxford/Neutrophils-Classifier-App
Project-URL: Issues, https://github.com/bpi-oxford/Neutrophils-Classifier-App/issues
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: neutrophils-core==0.1.1
Requires-Dist: PyQt5>=5.15.0
Requires-Dist: PyQtWebEngine
Requires-Dist: numpy>=1.21.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: scikit-learn>=1.0.0
Requires-Dist: matplotlib>=3.5.0
Requires-Dist: seaborn>=0.11.0
Requires-Dist: vtk>=9.0.0
Requires-Dist: qdrant-client>=1.0.0
Requires-Dist: Pillow>=8.3.0
Requires-Dist: tqdm>=4.62.0
Requires-Dist: pyqtgraph>=0.13.3
Requires-Dist: mdit_py_plugins
Requires-Dist: umap-learn>=0.5.5
Dynamic: license-file

# Neutrophils Maturation Classifier App

![alt text](./doc/screenshot.png "Screenshot")

A minimal 3D neutrophil maturation classification app with convolution neural network.

## Overview

This application allows for the automated classification of neutrophils at different maturation stages using a 3D convolutional neural network. It's designed to assist researchers and clinicians in analyzing 3D neutrophil morphology with geometric and CNN embedded features.

**Note**: GPU runtime only available on Linux.

## Features

- 3D visualization of neutrophil isosurfaces
- Real-time classification of neutrophil maturation stages
- Support for TIFF image input
- Batch processing capabilities

## Requirements

- Python 3.9 or higher
- CUDA-compatible GPU (recommended for GPU acceleration)

## Installation

### Simple Installation (Recommended)
```bash
pip install neutrophils-classifier
```

**Note**: This package now uses the published `neutrophils-core` library from PyPI, which provides the core machine learning functionality.

### Run the App
```bash
neutrophil-classifier
```

## For Developers

### Development Setup
1. Set up the conda environment:
```bash
git clone git@github.com:bpi-oxford/Neutrophils-Classifier-App.git
cd Neutrophils-Classifier-App
git submodule update --init --recursive
mamba env create -f env-minimal.yaml
mamba activate neutrophils-minimal
```

2. Install in editable mode:
```bash
pip install -e .
```

3. Run the application:
```bash
neutrophil-classifier
```

### Building and Publishing

See [`BUILD_GUIDE.md`](BUILD_GUIDE.md) for detailed build and publish instructions.
