{"id":27371695,"url":"https://github.com/pytomography/slicerspectrecon","last_synced_at":"2025-04-13T09:44:23.471Z","repository":{"id":243896231,"uuid":"707575209","full_name":"PyTomography/SlicerSPECTRecon","owner":"PyTomography","description":"A 3D Slicer extension for SPECT reconstruction, built using PyTomography","archived":false,"fork":false,"pushed_at":"2025-03-31T17:14:48.000Z","size":174167,"stargazers_count":21,"open_issues_count":3,"forks_count":8,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-11T11:24:30.730Z","etag":null,"topics":["3d-slicer-extension","image-reconstruction"],"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/PyTomography.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-10-20T07:49:15.000Z","updated_at":"2025-03-31T17:14:52.000Z","dependencies_parsed_at":"2024-08-08T06:35:54.568Z","dependency_job_id":"d68f3e91-7b66-43fc-a287-82dcdf68663f","html_url":"https://github.com/PyTomography/SlicerSPECTRecon","commit_stats":null,"previous_names":["qurit/slicer_spect_recon","pytomography/slicer_spect_recon","pytomography/slicer","pytomography/slicerspectrecon"],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PyTomography%2FSlicerSPECTRecon","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PyTomography%2FSlicerSPECTRecon/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PyTomography%2FSlicerSPECTRecon/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PyTomography%2FSlicerSPECTRecon/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PyTomography","download_url":"https://codeload.github.com/PyTomography/SlicerSPECTRecon/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248694162,"owners_count":21146944,"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":["3d-slicer-extension","image-reconstruction"],"created_at":"2025-04-13T09:44:22.789Z","updated_at":"2025-04-13T09:44:23.457Z","avatar_url":"https://github.com/PyTomography.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SPECT Tomographic Reconstruction 3D Slicer Extension\r\n\r\nThis is the official repository for the `Slicer` extension `SlicerSPECTRecon`. **For details on how to use, see the [user manual](https://github.com/PyTomography/Slicer/blob/main/User_Manual.md) and the [associated youtube video tutorial](https://www.youtube.com/watch?v=DzV1soWTzEA)**\r\n\r\nThis module enables the reconstruction of raw SPECT projection data, providing customizable options for image modeling and image reconstruction. The module has a SIMIND to DICOM converter to permit reconstruction of SIMIND Monte Carlo data.\r\n\r\nThe module is divided into the following sections:\r\n\r\n- Data Converters: Provides tools for converting data from various sources into the DICOM format.\r\n- Input Data: Users can select data from multiple bed positions after loading the projection data into the 3D Slicer DICOM database. \r\n- System Modeling: Allows users to define transforms that are used to build the system matrix.\r\n- Likelihood: Allows users to choose their preferred likelihood function.\r\n- Reconstruction Algorithm: Provides the option of selecting a preferred reconstruction algorithm and their associated parameters\r\n\r\nPlease refer to the `User_Manual.md` file for further information\r\n\r\n## User interface\r\nWithin Slicer, the \"SPECT reconstruction\" module is located under the parent category \"Tomographic Reconstruction\". For more details, see the [user manual](https://github.com/PyTomography/Slicer/blob/main/User_Manual.md)\r\n\r\n- Inputs\r\n  - SPECT projection data\r\n  - (optional) CT data for attenuation correction\r\n- Outputs\r\n  - a 3D reconstruction SPECT image. The volume will be saved under the specified name (or as the dataset name appended with _reconstructed) and will be located within the Subject Hierarchy in the Data Module.\r\n\r\n## Resources\r\n\r\nThe following link collection should facilitate understanding the code in this extension:\r\n\r\n- [Slicer Utils](https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/util.py)\r\n- [DICOM Introduction](https://www.slicer.org/wiki/Documentation/Nightly/FAQ/DICOM)\r\n- [DICOM Structure](https://www.slicer.org/wiki/Documentation/4.0/Modules/CreateDICOMSeries)\r\n- [DICOM Browser](https://dicom.innolitics.com/ciods)\r\n- [Subject Hierarchy](https://www.slicer.org/wiki/Documentation/4.5/Modules/SubjectHierarchy)\r\n\r\n## Sample Data\r\n\r\nThe links to the example data (sample patient and simind files) are in the sample_data.txt file in the `Resources` folder. \r\n\r\n## Contribute\r\n\r\nIf you'd like to contribute, you can find an orientation on the Slicer [documentation for developers](https://www.slicer.org/wiki/Documentation/Nightly/Developers).\r\n\r\nPlease read first the `CONTRIBUTING.md` file for further information on how to contribute. You can also check the Pytomography [readthedocs](https://pytomography.readthedocs.io/en/latest/) for an orientation on Pytomography.\r\n\r\n## License\r\n\r\nSlicerSPECTRecon is subject to the `MIT License`, which is in the project's root.\r\n\r\n## Contact\r\n\r\nPlease post any questions to the [Pytomography Discourse Forum](https://pytomography.discourse.group/).\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpytomography%2Fslicerspectrecon","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpytomography%2Fslicerspectrecon","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpytomography%2Fslicerspectrecon/lists"}