https://github.com/henriqueslab/rescale4dl
ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation
https://github.com/henriqueslab/rescale4dl
Last synced: 9 months ago
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ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation
- Host: GitHub
- URL: https://github.com/henriqueslab/rescale4dl
- Owner: HenriquesLab
- License: mit
- Created: 2023-10-18T09:09:57.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2025-04-24T09:23:01.000Z (about 1 year ago)
- Last Synced: 2025-04-24T10:28:11.124Z (about 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 16.6 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation
[](https://www.python.org/downloads/)
[](https://opensource.org/licenses/MIT)
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:
```terminal
conda create -n rescale4dl "python<=3.12"
conda activate rescale4dl
```
Install ReScale4DL with `pip`:
```terminal
pip install rescale4dl
```
### Manual installation
Manual installation using the GitHub repository
```terminal
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`](https://github.com/HenriquesLab/ReScale4DL/blob/main/Notebooks/Rescale_Images.ipynb)
### 2. Segmentation Analysis
Notebook: [`Evaluate_Segmentation.ipynb`](https://github.com/HenriquesLab/ReScale4DL/blob/main/Notebooks/Evaluate_Segmentation.ipynb)
### 3. Rescale and crop
Notebook: [`Rescale_Foundation_Models.ipynb`](https://github.com/HenriquesLab/ReScale4DL/blob/main/Notebooks/Rescale_Foundation_Models.ipynb)
## Contributing
We welcome contributions through:
- [Issue reporting](https://github.com/HenriquesLab/ReScale4D/issues)
- [Pull requests](https://github.com/HenriquesLab/ReScale4D/pulls)
## License
MIT License - See [LICENSE](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](https://doi.org/10.1101/2025.04.09.647871)
[](https://www.biorxiv.org/content/10.1101/2025.04.09.647871v1)
```
@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
}
```