sirf

Main repository for the CCP SynerBI software

https://github.com/synerbi/sirf

Science Score: 75.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Academic email domains
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Institutional organization owner
Organization synerbi has institutional domain (www.ccpsynerbi.ac.uk)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.3%) to scientific vocabulary

Keywords

image-reconstruction medical-imaging pet-mr

Last synced: 10 months ago · JSON representation ·

Repository

Main repository for the CCP SynerBI software

Basic Info

Host: GitHub
Owner: SyneRBI
License: other
Language: C++
Default Branch: master
Homepage: http://www.ccpsynerbi.ac.uk
Size: 9.65 MB

Statistics

Stars: 65
Watchers: 22
Forks: 29
Open Issues: 165
Releases: 16

Topics

image-reconstruction medical-imaging pet-mr

Created over 9 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Contributing License Citation Notice

Synergistic Image Reconstruction Framework

This software is the main output of SyneRBI, the Collaborative Computational Platform for Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR).

Please start with our latest User's Guide.

How to obtain SIRF

There are multiple ways to obtain a binary version of SIRF, please check them out in our documentation page how to obtain SIRF or our Wiki page for installation instructions.

Where is everything installed?

SIRF largely follows the usual directory structure with some minor tweaks. When using the default options when building SIRF, you will get (most of the) following, depending what was found/built: <install-dir>/ bin/ # executables lib/ # libraries python/ # Python files matlab/ # MATLAB files share/SIRF-V.v/ # versioned location (e.g. SIRF-3.0) doc/ # doxumentation doxygen/ # C++ documentation files generated by doxygen examples/ # example scripts data/ # data used in example scripts

Owner

Name: SyneRBI
Login: SyneRBI
Kind: organization
Location: United Kingdom

Website: http://www.ccpsynerbi.ac.uk
Repositories: 6
Profile: https://github.com/SyneRBI

Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: SIRF Synergistic Image Reconstruction Framework
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Evgueni
    family-names: Ovtchinnikov
    orcid: 'https://orcid.org/0000-0002-9359-6514'
    affiliation: UK Research & Innovation
  - given-names: Richard
    family-names: Brown
    affiliation: University College London
    orcid: 'https://orcid.org/0000-0001-6989-9200'
  - given-names: Johannes
    family-names: Mayer
    affiliation: Physikalisch-Technische Bundesanstalt (PTB)
    orcid: 'https://orcid.org/0000-0002-2500-445X'
  - given-names: Edoardo
    family-names: Pasca
    affiliation: UK Research & Innovation
    orcid: 'https://orcid.org/0000-0001-6957-2160'
  - given-names: Casper
    family-names: da Costa-Luis
    affiliation: King's College London
    orcid: 'https://orcid.org/0000-0002-7211-1557'
  - given-names: David
    family-names: Atkinson
    affiliation: University College London
    orcid: 'https://orcid.org/0000-0003-1124-6666'
  - given-names: Christoph
    family-names: Kolbitsch
    orcid: 'https://orcid.org/0000-0002-4355-8368'
    affiliation: Physikalisch-Technische Bundesanstalt (PTB)
  - given-names: Nikos
    family-names: Efthimiou
    orcid: 'https://orcid.org/0000-0003-1947-5033'
  - given-names: Imraj
    family-names: Singh
    orcid: 'https://orcid.org/0000-0003-2186-0977'
    affiliation: University College London
  - given-names: Matthew
    family-names: Strugari
    affiliation: Dalhousie University (Canada)
  - given-names: Ashley
    family-names: Gillman
    orcid: 'https://orcid.org/0000-0001-9130-1092'
    affiliation: >-
      Commonwealth Scientific and Industrial Research
      Organisation, and University of Queensland
  - orcid: 'https://orcid.org/0000-0002-1815-4716'
    affiliation: University College London, National Physics Laboratory
    family-names: Porter
    given-names: Sam David
  - given-names: Daniel
    family-names: Deidda
    affiliation: National Physical Laboratory (UK)
    orcid: 'https://orcid.org/0000-0002-2766-4339'
  - given-names: Ander
    family-names: Biguri
    orcid: 'https://orcid.org/0000-0002-2636-3032'
    affiliation: University College London
  - given-names: Toni
    family-names: Reeves
    orcid: 'https://orcid.org/0000-0002-9151-3295'
    affiliation: University College London
  - given-names: Alexander
    family-names: Whitehead
  - family-names: skarrea
  - given-names: Evangelos
    family-names: Papoutsellis
    affiliation: UK Research & Innovation
  - family-names: Fardell
    given-names: Gemma
    orcid: 'https://orcid.org/0000-0003-2388-5211'
    affiliation: UK Research & Innovation
  - affiliation: University College London
    family-names: Thomas
    given-names: Ben
    orcid: 'https://orcid.org/0000-0002-9784-1177'
  - family-names: Zhong
    given-names: Shenjun
  - orcid: 'https://orcid.org/0000-0003-2919-1894'
    affiliation: University College London
    given-names: Francesca
    family-names: Leek
  - orcid: 'https://orcid.org/0000-0001-8523-353X'
    affiliation: University of Bath
    given-names: Matthias
    family-names: Ehrhardt
  - orcid: 'https://orcid.org/0000-0002-5514-199X'
    affiliation: University College London
    family-names: Thielemans
    given-names: Kris
identifiers:
  - type: doi
    value: 10.5281/zenodo.2707911
    description: >-
      The concept DOI of the work (DOI for all
      versions).
  - type: doi
    value: 10.1016/j.cpc.2019.107087
    description: >-
      "SIRF: Synergistic Image Reconstruction
      Framework". Computer Physics Communications
      Volume 249, April 2020, 107087
  - type: doi
    value: 10.1098/rsta.2020.0208
    description: >-
      "Motion estimation and correction for
      simultaneous PET/MR using SIRF and CIL". Philos
      Trans A Math Phys Eng Sci . 2021 Aug
      23;379(2204):20200208.
  - type: doi
    value: 10.1109/NSSMIC.2017.8532815
    description: >-
      "SIRF: Synergistic Image Reconstruction
      Framework". 2017 IEEE Nuclear Science Symposium
      and Medical Imaging Conference (NSS/MIC)
repository-code: 'https://github.com/SyneRBI/SIRF'
keywords:
  - pet-mr
  - spect
  - medical imaging
  - image reconstruction
  - synergistic reconstruction
license: Apache-2.0

GitHub Events

Total

Create event: 12
Commit comment event: 3
Issues event: 23
Watch event: 6
Delete event: 9
Issue comment event: 109
Push event: 106
Gollum event: 22
Pull request review event: 201
Pull request review comment event: 240
Pull request event: 31

Last Year

Create event: 12
Commit comment event: 3
Issues event: 23
Watch event: 6
Delete event: 9
Issue comment event: 109
Push event: 106
Gollum event: 22
Pull request review event: 201
Pull request review comment event: 240
Pull request event: 31

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 137
Total pull requests: 119
Average time to close issues: 8 months
Average time to close pull requests: 7 months
Total issue authors: 20
Total pull request authors: 14
Average comments per issue: 2.18
Average comments per pull request: 3.33
Merged pull requests: 81
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 16
Pull requests: 27
Average time to close issues: 19 days
Average time to close pull requests: 9 days
Issue authors: 7
Pull request authors: 4
Average comments per issue: 0.38
Average comments per pull request: 2.04
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

KrisThielemans (73)
evgueni-ovtchinnikov (16)
paskino (9)
johannesmayer (8)
samdporter (6)
epapoutsellis (4)
ckolbPTB (3)
NicoleJurjew (2)
Letizia97 (2)
maddin200 (2)
varzakis (2)
Imraj-Singh (2)
danieldeidda (2)
casperdcl (1)
rijobro (1)

Pull Request Authors

evgueni-ovtchinnikov (63)
KrisThielemans (49)
paskino (8)
rijobro (8)
johannesmayer (5)
danieldeidda (3)
ashgillman (2)
Imraj-Singh (2)
samdporter (2)
ALEXJAZZ008008 (1)
casperdcl (1)
mastergari (1)
ckolbPTB (1)
rmapree (1)

Top Labels

Issue Labels

enhancement (12) bug (12) STIR (4) SIRF/CIL integration (3) design (2) external-fix-required (1) help wanted (1) request (1)

Pull Request Labels

enhancement (19) SIRF/CIL integration (6) in-progress (5) request (2) help wanted (1)

Dependencies

.github/workflows/build-test.yml actions

AndreMiras/coveralls-python-action develop composite
actions/checkout v2 composite
hendrikmuhs/ccache-action v1 composite

ci-requirements.txt pypi

coverage *
coveralls *

requirements.txt pypi

deprecation *
docopt *
matplotlib--only-binary =matplotlib
nibabel *
numpy >=1.18.0
psutil *
pytest *
pytest-cov *
scipy--only-binary =scipy

ecosyste.ms

Data

Tools

Indexes

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Experiments

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