{"id":26509941,"url":"https://github.com/radxtools/radpathfusion","last_synced_at":"2025-08-01T19:33:13.472Z","repository":{"id":102189921,"uuid":"299681135","full_name":"radxtools/radpathfusion","owner":"radxtools","description":"Jupyter notebook with Python-based workflow for co-registration of radiographic imaging (MRI/CT etc.) with digitized pathology images, and mapping annotations from pathology onto imaging.","archived":false,"fork":false,"pushed_at":"2022-10-05T01:00:24.000Z","size":104140,"stargazers_count":4,"open_issues_count":4,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-04-06T18:13:41.216Z","etag":null,"topics":["cancer-imaging-research","computational-imaging","digital-pathology","docker","image-registration","itcr","python","radiology","radiomics"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/radxtools.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":"2020-09-29T16:53:24.000Z","updated_at":"2024-03-20T03:35:10.000Z","dependencies_parsed_at":null,"dependency_job_id":"cf9c1866-69d2-48f9-b54c-dc1dd35558d6","html_url":"https://github.com/radxtools/radpathfusion","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/radxtools/radpathfusion","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/radxtools%2Fradpathfusion","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/radxtools%2Fradpathfusion/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/radxtools%2Fradpathfusion/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/radxtools%2Fradpathfusion/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/radxtools","download_url":"https://codeload.github.com/radxtools/radpathfusion/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/radxtools%2Fradpathfusion/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268286758,"owners_count":24226124,"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","status":"online","status_checked_at":"2025-08-01T02:00:08.611Z","response_time":67,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["cancer-imaging-research","computational-imaging","digital-pathology","docker","image-registration","itcr","python","radiology","radiomics"],"created_at":"2025-03-21T01:38:23.063Z","updated_at":"2025-08-01T19:33:13.440Z","avatar_url":"https://github.com/radxtools.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Overview\n\nThis notebook provides an interactive workflow to load in a radiographic imaging volume (MRI, CT, etc.) with a corresponding digitized pathology image, and go through co-registration to map one onto the other. Functionalities include selecting corresponding sections, basic image manipulation and scaling as pre-processing steps, as well as selecting corresponding landmarks to run a deformable co-registration between the modalities. The deformation can then be applied to any annotation to map it from one to the other (e.g. map cancer annotation from pathology image onto MR image) within the noteboo. Results are visualized and fully editable and updatable within the notebook workflow.\n\n# References\nIf you make use of this implementation, please cite the following paper:\n\nAntunes, JT, Viswanath, SE, Brady, JT, Crawshaw, B, Ros, P, Steele, S, Delaney, CP, Paspulati, RM, Willis, JE, Madabhushi, A, \"Coregistration of Preoperative MRI with Ex Vivo Mesorectal Pathology Specimens to Spatially Map Post-treatment Changes in Rectal Cancer Onto In Vivo Imaging: Preliminary Findings\", Acad Radiol, 2018 Jul;25(7):833-841.  \n\n\n## Prerequisites\n\nThe below software and configurations will be needed to execute the notebooks:\n\n* Docker\n    * Update docker with 8 gigs of memory\n* git\n\n\n# Getting started with Rad Path Fusion\n\n## Running with docker\n\nFirst clone this repository\n\n```\ngit clone https://github.com/Theta-Tech-AI/radpathfusion.git\n```\n\nSecond, we will quickly configure the docker memory\n\n## Docker Setup:\n1. Open Docker Destop\n2. Open settings\n2. Click on resources as seen on the below screen shot\n4. Move the memory limit to 8 GB\n![Docker Configuration](assets/docker_config.png)\n\nLastly, we will run the docker image using either:\n\n1. docker-compose\n2. docker run\n\n### docker-compose\n\nRun the following commands to start the docker container\n\n```\ncd docker\ndocker-compose up\n```\n\n### docker run\n\nWith this step, you don't need to clone the url.\nRun the following commands to start the docker container\n\n```\ndocker rm radxtools/radpathfusion-examples\ndocker pull radxtools/radpathfusion-examples\ndocker run -d -p 3000:3000 --name radpathfusion-examples radxtools/radpathfusion-examples\n```\n\n## Tutorials\n\nOnce the docker image is up and running. You can view our notebooks. You can get started with the notebook to learn how to use the package. You should start with `notebooks/Rad Path Fusion Final.ipynb`\n\nThe notebooks can be viewed by opening the browser and visting the url http://localhost:3000\n\nA walk through of the notebook with screen shots can be found [here](/docs/notebook_starter.md)\n\n\n# Contribution Guide:\n\nPlease follow google style formatting for [docstrings](https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings)\n\n## Bugs and Feature Request\n\nPlease submit bugs and features to our github page.\n\n\n## Pull Requests\nCreate a issue on our board.\nCreate a pull request with your changes. Tag your changes with the issue number (commit message should have issue number).\nSomeone from the team will review your request and merge your changes for the next release.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fradxtools%2Fradpathfusion","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fradxtools%2Fradpathfusion","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fradxtools%2Fradpathfusion/lists"}