{"id":17284321,"url":"https://github.com/fepegar/vesseg","last_synced_at":"2025-02-25T05:33:42.782Z","repository":{"id":38827238,"uuid":"159247404","full_name":"fepegar/vesseg","owner":"fepegar","description":"Brain vessel segmentation using 3D convolutional neural networks","archived":true,"fork":false,"pushed_at":"2022-06-23T17:55:20.000Z","size":2575,"stargazers_count":42,"open_issues_count":0,"forks_count":10,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-12T15:18:15.562Z","etag":null,"topics":["brain-vessel-segmentation","cnn","convolutional-neural-networks","deep-learning","segmentation"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fepegar.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null}},"created_at":"2018-11-26T23:36:52.000Z","updated_at":"2025-01-11T07:01:45.000Z","dependencies_parsed_at":"2022-08-31T04:40:55.267Z","dependency_job_id":null,"html_url":"https://github.com/fepegar/vesseg","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fepegar%2Fvesseg","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fepegar%2Fvesseg/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fepegar%2Fvesseg/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fepegar%2Fvesseg/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fepegar","download_url":"https://codeload.github.com/fepegar/vesseg/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240612485,"owners_count":19829026,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["brain-vessel-segmentation","cnn","convolutional-neural-networks","deep-learning","segmentation"],"created_at":"2024-10-15T09:53:48.104Z","updated_at":"2025-02-25T05:33:42.319Z","avatar_url":"https://github.com/fepegar.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Vesseg\n\nBrain vessel segmentation from digital subtraction angiography (DSA) using a 3D convolutional neural network (CNN).\n\n![screenshot](screenshots/slicer.gif)\n(Brain parcellation performed using [GIF](https://spiral.imperial.ac.uk/bitstream/10044/1/30755/4/07086081.pdf), not included in this repository).\n\n## Installation\n\n### GPU support\n\nThis package uses [NiftyNet](https://github.com/NifTK/NiftyNet), which is built on top of [TensorFlow](https://www.tensorflow.org/), so first of all you need to follow the [instructions to setup your NVIDIA GPU](https://www.tensorflow.org/install/gpu).\n\nWhile it is possible to perform a segmentation without a GPU, inference of one large volume (512 × 512 × 394 voxels) using the default parameters takes one hour using CPU only and around 90 seconds using a GPU.\n\n### `vesseg` package\n\nUsing [`conda`](https://conda.io/docs/) is recommended:\n\n```shell\n$ conda create -n \"vesseg\" python=3.6 -y  # tensorflow doesn't support python 3.7 yet\n$ conda activate \"vesseg\"\n(vesseg) $ git clone \"https://github.com/fepegar/vesseg.git\" --depth 1\n(vesseg) $ pip install --editable \"./vesseg\"\n```\n\n## Usage\n\n```shell\n$ conda activate vesseg\n(vesseg) $ vesseg dsa_image.nii.gz dsa_vessels_seg.nii.gz\n(vesseg) $ bin2mesh dsa_vessels_seg.nii.gz dsa_vessels_mesh.vtp\n```\n\nTested on Linux and macOS.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffepegar%2Fvesseg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffepegar%2Fvesseg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffepegar%2Fvesseg/lists"}