This repository contains a biophysical model of the outer retina using Jaxley as described in our paper. Updates in progress 🛠️
After cloning the repository, it can be installed via
pip install jaxley-retinaFigure data that isn't included in the paper folder can be recreated by running the notebooks. Notebooks should bridge the gap between the scripts in the source code used to train the model and the code used to generate the final paper figures. Feel free to open Git issues or write me at [email protected] if you have any questions.
Phototransduction cascade stimuli and recordings can be downloaded here. For further information see the related paper Chen et al. 2024.
Original glutamate release data can be downloaded here. This data was further processed and traces were selected for training the ribbon synapse model in the code in this repository.
@article{kadhim2025data,
title={A data and task-constrained mechanistic model of the mouse outer retina shows robustness to contrast variations},
author={Kadhim, Kyra L and Beck, Jonas and Huang, Ziwei and Macke, Jakob H and Rieke, Fred and Euler, Thomas and Deistler, Michael and Berens, Philipp},
journal={bioRxiv},
year={2025},
publisher={Cold Spring Harbor Laboratory}
}