AutoMorph 2022 👀

--Code for AutoMorph: Automated Retinal Vascular Morphology Quantification via a Deep Learning Pipeline.

Please contact ykzhoua@gmail.com or yukun.zhou.19@ucl.ac.uk if you have questions.

Project website: https://rmaphoh.github.io/projects/automorph.html

Talks on NIHR Moorfields BRC: https://moorfieldsbrc.nihr.ac.uk/case-study/research-report/

News 👀

2023-08-24 update: Added feature measurement for disc-centred images; removed unused files in M3 folders.

Pixel resolution

The units for vessel average width, disc/cup height and width, and calibre metrics are defined as microns. For it, we need to organise a resolution_information.csv which includes the pixel resolution information, which can be queried in FDA or Dicom files. Alternatively, some people use approximate value for every images, e.g., 0.008 for Topcon 3D-OCT.

If you don't use these features or care their units, you can just run following command after putting all images in the folder of ./images

python generate_resolution.py

Running AutoMorph

Running with Colab

Use the Google Colab and a free Tesla T4 gpu Colab link click.

Running on local/virtual machine

Install and use on your own machines LOCAL.md.

Running with Docker

Zero experience in Docker? No worries DOCKER.md.

Common questions

Memory/ram error

We use Tesla T4 (16Gb) and 32vCPUs (120Gb). When you meet memory/ram issue in running, try to decrease batch size:

./M1_Retinal_Image_quality_EyePACS/test_outside.sh -b=64 to smaller, e.g., 32 or 16.
./M2_Artery_vein/test_outside.sh --batch-size=8 to smaller
./M2_lwnet_disc_cup/test_outside.sh --batchsize=8 to smaller

Invalid results

In csv files, invalid values (e.g., optic disc segmentation failure) are indicated with -1.

Components

Vessel segmentation BF-Net
Image pre-processing EyeQ
Optic disc segmentation lwnet
Feature measurement retipy

Citation

@article{zhou2022automorph,
  title={AutoMorph: Automated Retinal Vascular Morphology Quantification Via a Deep Learning Pipeline},
  author={Zhou, Yukun and Wagner, Siegfried K and Chia, Mark A and Zhao, An and Xu, Moucheng and Struyven, Robbert and Alexander, Daniel C and Keane, Pearse A and others},
  journal={Translational vision science \& technology},
  volume={11},
  number={7},
  pages={12--12},
  year={2022},
  publisher={The Association for Research in Vision and Ophthalmology}
}

RudRho/AutoMorph