neutrophils-classifier-app 1.0.1

A GUI application for neutrophil classification using deep learning models

Neutrophils Maturation Classifier App

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)

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

neutrophil-classifier

For Developers

Development Setup

1. Set up the conda environment:

git clone [e-mail]: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:

pip install -e .

3. Run the application:

neutrophil-classifier

Building and Publishing

See BUILD_GUIDE.md for detailed build and publish instructions.