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Deep Generative Classification of Blood Cell Morphology

This repository contains the code accompanying the paper "Deep Generative Classification of Blood Cell Morphology", which is published as a preprint on arXiv and is currently under peer review. The code demonstrates the application of diffusion-based models for classification tasks, with a focus on blood cell morphology. It provides a foundation for reproducing key findings and offers a framework for further exploration in this area.

Key Features

• Generative Classification: Implements a diffusion-based classifier for robust and accurate blood cell classification.
• Anomaly Detection: Demonstrates superior anomaly detection capabilities compared to traditional discriminative models.
• Uncertainty Quantification: Provides reliable uncertainty estimates, allowing for better assessment of model predictions.
• Domain Shift Robustness: Exhibits resilience to variations in imaging conditions, enhancing generalisability.
• Data Efficiency: Achieves high performance even in low-data regimes, a crucial advantage in medical imaging.
• Explainability: Generates counterfactual heatmaps, providing interpretable insights into model decisions.

Getting Started

Prerequisites

• GPU: $\ge$ 24GB RAM (for smaller GPUs, decrease the batch size in EXAMPLE.sh)
• Operating System: Tested on Ubuntu 20.04.6 and Ubuntu 22.04.4
• CUDA: Tested on CUDA 11.8 and 12.5

Installation

1. Clone the repository:

   git clone git@github.com:Deltadahl/CytoDiffusion.git
   cd CytoDiffusion
   

2. Create and activate the conda environment:

   conda env create -f environment.yml
   conda activate CytoDiffusion
   

3. Configure Accelerate: Run the following command:

   accelerate config
   

   When prompted, provide these answers for a simple single GPU setup:

   • Compute environment: This machine
   • Machine type: No distributed training
   • Run training on CPU only: NO
   • Optimize script with torch dynamo: NO
   • Use DeepSpeed: NO
   • GPU(s) to use: 0
   • Enable numa efficiency: NO
   • Use mixed precision: fp16

4. Log in to Weights & Biases (wandb):

   wandb login
   

   Follow the prompts to complete the login process.

Running the Example Code

1. Prepare the example data:

   cd data/prepare_data
   python prepare_data.py
   

   Provide the path to example_data (located in the current folder) when prompted.

2. Train the model:

   cd ../../train_and_test
   sh EXAMPLE.sh
   

Using Your Own Dataset

To use your own dataset, provide the path to your dataset when you run prepare_data.py For example:

your_dataset
├── basophil
│   ├── image1.png
│   └── image2.png
├── eosinophil
│   ├── image3.png
│   └── image4.png
├── ...
└── name_to_number.json

Then, update the paths in the EXAMPLE.sh script accordingly.

Configuration and Reproducibility

We provide several options for configuring and running experiments:

1. Basic Configuration: For initial setup and testing, we recommend using the EXAMPLE.sh script located in the train_and_test folder. This script serves as a template for setting essential parameters such as data paths, training steps, and other relevant settings.

2. Reproducing Experiments: To facilitate the reproduction of our experimental results, we have included additional .sh scripts in the same folder as EXAMPLE.sh. These scripts contain the specific configurations used in our experiments.

3. Custom Experiments: Feel free to create your own .sh scripts based on our examples to explore different configurations and scenarios.

Running Experiments

To run any of these scripts, follow these steps:

1. Prepare the Data:

   • For EXAMPLE.sh, follow the data preparation steps in the "Getting Started" section.
   • For other experiment scripts or custom datasets: a. Navigate to the data preparation folder:

     cd data/prepare_data
     

     b. Run the data preparation script:

     python prepare_data.py
     

     c. When prompted, provide the path to your dataset.

2. Update Script Paths:

   • Open the .sh script you want to use.
   • Update the data paths in the script to match your prepared dataset location.

3. Run the Script:

   • Navigate to the train_and_test folder:

     cd ../../train_and_test
     

   • Execute the desired script:

     sh EXAMPLE.sh
     # or
     sh <sh_name>.sh
     

Datasets

The code is tested on the following datasets:

• PBC Dataset: Acevedo et al. A dataset of microscopic peripheral blood cell images for development of automatic recognition systems
• Raabin-WBC Dataset: Kouzehkanan et al. A large dataset of white blood cells containing cell locations and types, along with segmented nuclei and cytoplasm
• Bodzas Dataset: Bodzas et al. A high-resolution large-scale dataset of pathological and normal white blood cells
• Our Custom Dataset: See our paper

Expected Performance

The model achieves an accuracy of >80% when you run the example dataset. The EXAMPLE.sh script will save the trained model locally and log training information to Weights & Biases.

Contact

For questions or collaboration opportunities, please contact:
Simon Deltadahl: scfc3@cam.ac.uk

Reporting Issues

Please report any issues or bugs on the Issues page.

Licence

This code is licenced under the Apache 2.0 Licence.

Citation

If you use this code in your research, please cite our paper:

@article{deltadahl2024deep,
  title={Deep Generative Classification of Blood Cell Morphology},
  author={Deltadahl, Simon and Gilbey, Julian and Van Laer, Christine and Boeckx, Nancy and Leers, Mathie and Freeman, Tanya and Aiken, Laura and Farren, Timothy and Smith, Matt and Zeina, Mohamad and {BloodCounts! consortium} and Rudd, James HF and Piazzese, Concetta and Taylor, Joseph and Gleadall, Nicholas and Schönlieb, Carola-Bibiane and Sivapalaratnam, Suthesh and Roberts, Michael and Nachev, Parashkev},
  journal={arXiv preprint arXiv:2408.08982},
  year={2024}
}