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mrivis

mrivis: Medical image visualization library for neuroscience in python - Published in JOSS (2018)

https://github.com/raamana/mrivis

Science Score: 93.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

alignment checkerboard comparison mismatch mri neuroimaging neuroscience quality-control registration similarity visualization

Keywords from Contributors

connectivity network-analysis datascience mesh
Last synced: 6 months ago · JSON representation

Repository

medical image visualization library and development toolkit

Basic Info
Statistics
  • Stars: 23
  • Watchers: 3
  • Forks: 3
  • Open Issues: 10
  • Releases: 2
Topics
alignment checkerboard comparison mismatch mri neuroimaging neuroscience quality-control registration similarity visualization
Created about 8 years ago · Last pushed over 2 years ago
Metadata Files
Readme Contributing License Code of conduct Authors

README.rst 

------
mrivis
------

.. image:: http://joss.theoj.org/papers/10.21105/joss.00897/status.svg
   :target: https://doi.org/10.21105/joss.00897

.. image:: https://img.shields.io/pypi/v/mrivis.svg

.. image:: https://api.codacy.com/project/badge/Grade/370b1b78383b40b99eb15ae0490cfbdb
    :target: https://www.codacy.com/app/raamana/mrivis

.. image:: https://img.shields.io/badge/say-thanks-ff69b4.svg
        :target: https://saythanks.io/to/raamana


----------

`mrivis` offers intuitive high-level classes for visualization of medical imaging data including:

- advanced classes to easily develop customizable visualizations of 3D and 4D images, such as `Carpet()`, `SlicePicker()`, `Collage()` and the like
- tools for comparison of spatial alignment of two 3D MRI scans (T1, T2, PET etc) using checkerboard plots and other comparison methods
- additional helper, convenience and utility scripts related to visualization

Full documentation for both visualization classes and alignment check tools is available at

https://raamana.github.io/mrivis/readme.html

----------


A sample gallery of different ways to check alignment (just one of the many other features in `mrivis`) is shown below:

.. image:: docs/flyer_option_matrix.png

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Full documentation https://raamana.github.io/mrivis/readme.html

Executable and interactive demo for the visualization classes:

.. image:: https://mybinder.org/badge.svg
    :target: https://mybinder.org/v2/gh/raamana/mrivis/master?filepath=docs%2Fexample_notebooks%2Fmrivis_demo_vis_classes.ipynb


**Installation**

.. code-block:: console

    $ pip install mrivis


If you would like to use the export to GIF from ``SlicePicker``, then install the ``imageio`` package as well via ``pip install imageio``

Owner

  • Name: Pradeep Reddy Raamana
  • Login: raamana
  • Kind: user
  • Location: Pittsburgh, PA
  • Company: University of Pittsburgh

Neuroscientist trying to bridge the gap between clinic & computer science. Interests: Machine learning, Neuroimaging, Brain disorders, Informatics, Open science

JOSS Publication

mrivis: Medical image visualization library for neuroscience in python
Published
October 09, 2018
DOI
Volume 3, Issue 30, Page 897
Authors
Pradeep Reddy Raamana ORCID
Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
Stephen C. Strother ORCID
Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
Editor
Ariel Rokem ORCID
Tags
visualization neuroscience alignment neuroimaging multimodal development kit
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GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 248
  • Total Committers: 3
  • Avg Commits per committer: 82.667
  • Development Distribution Score (DDS): 0.173
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Pradeep Reddy Raamana r****a@g****m 205
Pradeep Reddy Raamana p****a@r****g 42
dependabot[bot] 4****] 1
Committer Domains (Top 20 + Academic)
research.baycrest.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 13
  • Total pull requests: 8
  • Average time to close issues: 4 days
  • Average time to close pull requests: 4 months
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 3.38
  • Average comments per pull request: 0.25
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • raamana (10)
  • lalet (1)
  • miykael (1)
  • glatard (1)
Pull Request Authors
  • raamana (5)
  • dependabot[bot] (3)
Top Labels
Issue Labels
Pull Request Labels
dependencies (3)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 170 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 2
  • Total versions: 13
  • Total maintainers: 1
pypi.org: mrivis

Intuitive high-level classes for visualization of medical imaging data

  • Versions: 13
  • Dependent Packages: 2
  • Dependent Repositories: 2
  • Downloads: 170 Last month
Rankings
Dependent packages count: 3.1%
Dependent repos count: 11.6%
Average: 12.7%
Stargazers count: 13.1%
Forks count: 16.8%
Downloads: 18.6%
Maintainers (1)
raamana
Last synced: 6 months ago