SlicerSPECTRecon
SlicerSPECTRecon: A 3D Slicer Extension for SPECT Image Reconstruction - Published in JOSS (2024)
Science Score: 36.0%
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Low similarity (14.6%) to scientific vocabulary
Keywords
Repository
A 3D Slicer extension for SPECT reconstruction, built using PyTomography
Basic Info
Statistics
- Stars: 24
- Watchers: 3
- Forks: 8
- Open Issues: 5
- Releases: 2
Topics
Metadata Files
README.md
SPECT Tomographic Reconstruction 3D Slicer Extension
This is the official repository for the Slicer extension SlicerSPECTRecon. For details on how to use, see the user manual and the associated youtube video tutorial
This 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.
The module is divided into the following sections:
- Data Converters: Provides tools for converting data from various sources into the DICOM format.
- Input Data: Users can select data from multiple bed positions after loading the projection data into the 3D Slicer DICOM database.
- System Modeling: Allows users to define transforms that are used to build the system matrix.
- Likelihood: Allows users to choose their preferred likelihood function.
- Reconstruction Algorithm: Provides the option of selecting a preferred reconstruction algorithm and their associated parameters
Please refer to the User_Manual.md file for further information
User interface
Within Slicer, the "SPECT reconstruction" module is located under the parent category "Tomographic Reconstruction". For more details, see the user manual
- Inputs
- SPECT projection data
- (optional) CT data for attenuation correction
- Outputs
- 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.
Resources
The following link collection should facilitate understanding the code in this extension:
Sample Data
The links to the example data (sample patient and simind files) are in the sample_data.txt file in the Resources folder.
Contribute
If you'd like to contribute, you can find an orientation on the Slicer documentation for developers.
Please read first the CONTRIBUTING.md file for further information on how to contribute. You can also check the Pytomography readthedocs for an orientation on Pytomography.
License
SlicerSPECTRecon is subject to the MIT License, which is in the project's root.
Contact
Please post any questions to the Pytomography Discourse Forum.
Owner
- Name: PyTomography
- Login: PyTomography
- Kind: organization
- Email: lukepolson@outlook.com
- Repositories: 1
- Profile: https://github.com/PyTomography
Python for tomographic image reconstruction
GitHub Events
Total
- Issues event: 5
- Watch event: 5
- Issue comment event: 1
- Push event: 4
- Pull request event: 10
Last Year
- Issues event: 5
- Watch event: 5
- Issue comment event: 1
- Push event: 4
- Pull request event: 10
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Obed Dzikunu | o****u@g****m | 95 |
| Luke Polson | l****n@o****m | 47 |
| Marcel Stimberg | m****g@s****r | 5 |
| Carlos F. Uribe | c****i | 2 |
| pearsomark | p****k@g****m | 1 |
| Andras Lasso | l****o@q****a | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 5
- Total pull requests: 14
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Total issue authors: 4
- Total pull request authors: 2
- Average comments per issue: 0.2
- Average comments per pull request: 0.0
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 14
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 4
- Pull request authors: 2
- Average comments per issue: 0.2
- Average comments per pull request: 0.0
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- akmal871026 (2)
- PegiMessi (1)
- LucasMorel43 (1)
- mikhailpaltsev (1)
Pull Request Authors
- lukepolson (13)
- lassoan (1)