{"id":37890005,"url":"https://github.com/bunpc/2023-scos","last_synced_at":"2026-01-16T16:55:37.601Z","repository":{"id":185132365,"uuid":"672077193","full_name":"BUNPC/2023-SCOS","owner":"BUNPC","description":"Communications Biology 2023 - Measuring human cerebral blood flow and brain function with fiber-based speckle contrast optical spectroscopy system","archived":false,"fork":false,"pushed_at":"2023-08-01T18:53:27.000Z","size":6425,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-10T01:30:29.560Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BUNPC.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2023-07-28T21:33:58.000Z","updated_at":"2023-08-01T13:11:43.000Z","dependencies_parsed_at":"2023-07-31T20:52:02.208Z","dependency_job_id":"8ac02941-be98-4839-ab83-a95b3059301a","html_url":"https://github.com/BUNPC/2023-SCOS","commit_stats":null,"previous_names":["bunpc/2023-scos-sow5-communications-biology","bunpc/2023-scos"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/BUNPC/2023-SCOS","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BUNPC%2F2023-SCOS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BUNPC%2F2023-SCOS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BUNPC%2F2023-SCOS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BUNPC%2F2023-SCOS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BUNPC","download_url":"https://codeload.github.com/BUNPC/2023-SCOS/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BUNPC%2F2023-SCOS/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28480081,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2026-01-16T16:55:37.530Z","updated_at":"2026-01-16T16:55:37.590Z","avatar_url":"https://github.com/BUNPC.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SCOS data processing\n\nCommunications Biology 2023 - Measuring human cerebral blood flow and brain function with fiber-based speckle contrast optical spectroscopy system\n\nWe created a data analysis pipeline for SCOS under photon starved conditions. This repository contains:\n\n1) Sample speckle images and dark camera image from Hamamatsu ORCA-Fusion camera (./sample data)\n2) Camera parameters such as gain and mask (./camera calibration)\n3) Functions and script to run the noise correction pipeline\n\nTo run the code:\n\n1) Download all the files and subfolders in one folder\n2) Run HamamatsuPipeline.m\n\nThe HamamatsuPipeline.m outputs: \n\n1) Processed data files (img_file_mean_img.mat, analyzed_K2_img_file_YYYY_MM_DD_HH_mm.mat) in ./sample data.\n2) Raw standard deviation and mean intensity time course   \n   \u003cimg width=\"537\" alt=\"Screenshot 2023-08-01 at 1 01 13 PM\" src=\"https://github.com/BUNPC/2023-SCOS/assets/55467463/4ddceb44-6f8d-41f6-8597-b59867c97461\"\u003e\n3) Linear estimation of window I(t) in the contrast measurement\n   \u003cimg width=\"540\" alt=\"Screenshot 2023-08-01 at 1 01 35 PM\" src=\"https://github.com/BUNPC/2023-SCOS/assets/55467463/6443c906-7d1e-40f4-bada-4362fe3dd914\"\u003e\n4) Contribution of noise sources to the measured speckle contrast\n   \u003cimg width=\"539\" alt=\"Screenshot 2023-08-01 at 1 01 53 PM\" src=\"https://github.com/BUNPC/2023-SCOS/assets/55467463/d70cc54a-b65f-4537-9e13-c04fab0c9bad\"\u003e\n   \n5) Fundamental speckle contrast after noise correction and the corresponding blood flow index\n\n   \u003cimg width=\"543\" alt=\"Screenshot 2023-08-01 at 1 02 06 PM\" src=\"https://github.com/BUNPC/2023-SCOS/assets/55467463/578c7c4f-e610-4b15-a806-f895a126be78\"\u003e\n\nFor any issue reporting or suggestions, please contact Byungchan Kim, kennykim@bu.edu\n\n\n[![DOI](https://zenodo.org/badge/672077193.svg)](https://zenodo.org/badge/latestdoi/672077193)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbunpc%2F2023-scos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbunpc%2F2023-scos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbunpc%2F2023-scos/lists"}