Are retinal vasculature features altered in Amblyopia?

Authors

Rijul S. Soans, PhD
Susana T. L. Chung, OD, PhD

Sight Enhancement Laboratory (SELAB)
Herbert Wertheim School of Optometry & Vision Science
University of California, Berkeley, USA.

Publication

Soans, R. S. & Chung, S. T. L. (2026). Altered retinal vasculature in amblyopia. Vision Research, 242(108780), 1–12.
🔗 https://doi.org/10.1016/j.visres.2026.108780

Features

• Companion code for our research showing altered retinal vasculature in amblyopia - even in the fellow eye that sees better.
• Precise retinal vessel segmentation using Spatial Attention-UNet (SA-UNet paper)

Software Dependencies

The framework requires the following software:

• Python 3.9.2 - General purpose programming language for Vessel Segmentation
• MATLAB R2022b - Programming & Numeric Computing platform for Analyses

Getting Started

1. Install Python from the link provided above.
2. Install MATLAB from the link provided above.
3. Clone this repository.
4. Install dependencies for Python by: pip install -r requirements.txt OR for conda users:

   conda env create -f environment.yml
   conda activate amblyopia_iroct_env
   

5. Run the segmentation on an example image:

   python scripts/run_segmentation.py --image sample-images/AMB_001_OS.png --model models/SA_UNet.h5
   

6. If you want to segment all images at once:

   python -c "import glob,subprocess,sys;[subprocess.run([sys.executable,'scripts/run_segmentation.py','--image',f,'--model','models/SA_UNet.h5']) for f in glob.glob('sample-images/*.png')]"
   

7. To get the vasculature metrics for a particular segmented image, use MATLAB to open and run vessel_map_analyzer.m found under the scripts folder.

License

MIT License

Copyright 2025 © Rijul S. Soans, © Susana T. L. Chung

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.