ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation

A systematic approach for determining optimal image resolution in deep learning-based microscopy segmentation, balancing accuracy with acquisition/storage costs. Following this approach, researchers can improve the sustainability and cost-effectiveness of bioimaging studies by reducing data and computing needs while optimising microscopy techniques.

Key Features

• Resolution simulation: Rescale images and their respective annotations (upsample and downsample)
• Segmentation evaluation: Compare performance across resolutions using:
  • Mean Intersection-over-Union (IoU)
  • Morphological features
  • Potential throughput
  • Personalised metrics
• Visualization tools: Generate comparative plots and sample outputs

Installation

ReScale4DL is available as a Python package through pip. Activate your conda environment or create one:

conda create -n rescale4dl "python<=3.12"
conda activate rescale4dl

Install ReScale4DL with pip:

pip install rescale4dl

Manual installation

Manual installation using the GitHub repository

git clone https://github.com/HenriquesLab/ReScale4DL.git
cd rescale4dl
conda create -n rescale4dl "python<=3.12"
conda activate rescale4dl
python -m pip install .

Usage

1. Image Rescaling

Notebook: Rescale_Images.ipynb

2. Segmentation Analysis

Notebook: Evaluate_Segmentation.ipynb

3. Rescale and crop

Notebook: Rescale_Foundation_Models.ipynb

Contributing

We welcome contributions through:

• Issue reporting
• Pull requests

License

MIT License - See LICENSE for details

How to cite this work

Ferreira, M.G., Saraiva, B.M., Brito, A.D., Pinho, M.G., Henriques, R. and Gómez-de-Mariscal, E., ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation. bioRxiv, pp.2025-04, (2025) https://doi.org/10.1101/2025.04.09.647871

@article{ferreira2025rescale4dl,
  title={ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation},
  author={Ferreira, Mariana G and Saraiva, Bruno M and Brito, Ant{\'o}nio D and Pinho, Mariana G and Henriques, Ricardo and G{\'o}mez-de-Mariscal, Estibaliz},
  journal={bioRxiv},
  pages={2025--04},
  year={2025},
  publisher={Cold Spring Harbor Laboratory},
  URL = https://doi.org/10.1101/2025.04.09.647871
}