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retistruct

Computational reconstruction and transformation of flattened retinae

https://github.com/davidcsterratt/retistruct

Science Score: 36.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
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    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Computational reconstruction and transformation of flattened retinae

Basic Info
Statistics
  • Stars: 8
  • Watchers: 4
  • Forks: 8
  • Open Issues: 15
  • Releases: 12
Created over 11 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

Retistruct

computational reconstruction and transformation of flattened retinae

Retistruct is an R package to morph a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (a standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8° of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates.

For full details, including how to install from CRAN, go to the Retistruct home page.

Installation from Github

Install the devtoools package to enable installation from Github

First, from the R console, install the devtools package by typing: install.packages("devtools") followed by Return. This command will take some time to run, as it has to install a number of packages that it depends on.

Install Retistruct

Then, do one of the following from the R console:

  • To install the latest development branch (not yet released on CRAN): devtools::install_github("davidcsterratt/retistruct", subdir="pkg/retistruct") The development User guide has more details on how to use the new features.

  • To install from the stable branch (incremental improvements not yet released to CRAN), use the R devtools package like this: devtools::install_github("davidcsterratt/retistruct@v0.8.x", subdir="pkg/retistruct")

  • To install the current stable version, use the R devtools package like this: devtools::install_github("davidcsterratt/retistruct@v0.8.1", subdir="pkg/retistruct") You will need to replace 0.8.1 with the version number of the latest release.

Roadmap

There are a number of improvements on the horizon - see the list of milestones for full details.

Retistruct is not my main work at present, so improvements may take some time. Nevertheless, if there's something you'd like implemented, please let me know, either by creating an issue, or by email.

Funding Acknowledgements

The development of the initial version of Retistruct was supported by a Programme Grant from the UK Wellcome Trust (G083305) from 2008-2013.

Improvements to image handing and refactoring the code (released in v0.6.0) were supported by The Jackson Laboratory (Bar Harbor, ME, USA) Scientific Services Innovation Fund from 2016-2017 and an NIH R21 grant (EY027894) from 2018-2020 to Dr. Mark P. Krebs, The Jackson Laboratory.

The capabilities to reconstruct tissue comprised of separate fragments (released in v0.7.0) and to reconstruct 3D data comprising an overhead image and depth map (released in v0.7.2), and user interface improvements (released in v0.7.0) were supported by an NIH R21 grant (EY027894) from 2018-2020 to Dr. Mark P. Krebs, The Jackson Laboratory.

Owner

  • Name: David C Sterratt
  • Login: davidcsterratt
  • Kind: user
  • Company: University of Edinburgh

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 37
  • Watch event: 1
  • Issue comment event: 21
  • Push event: 27
  • Pull request review event: 10
  • Pull request review comment event: 7
  • Pull request event: 8
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 37
  • Watch event: 1
  • Issue comment event: 21
  • Push event: 27
  • Pull request review event: 10
  • Pull request review comment event: 7
  • Pull request event: 8

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 1,582
  • Total Committers: 8
  • Avg Commits per committer: 197.75
  • Development Distribution Score (DDS): 0.326
Top Committers
Name Email Commits
sterratt@INF.ED.AC.UK s****t@I****K@e****b 1,067
dcs d****s@e****b 204
David C Sterratt d****t@e****k 202
sterratt s****t@e****b 103
Brian Cohn b****2@g****m 3
Brian Cohn b****n@u****m 1
(no author) (****)@e****b 1
stefan7th s****h@e****b 1
Committer Domains (Top 20 + Academic)
ed.ac.uk: 1 inf.ed.ac.uk: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 18
  • Total pull requests: 5
  • Average time to close issues: 3 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.56
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 17
  • Pull requests: 5
  • Average time to close issues: 7 days
  • Average time to close pull requests: 3 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.59
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • davidcsterratt (18)
Pull Request Authors
  • JanOkul (5)
Top Labels
Issue Labels
bug (3) enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 240 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 4
  • Total versions: 10
  • Total maintainers: 1
cran.r-project.org: retistruct

Retinal Reconstruction Program

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 4
  • Downloads: 240 Last month
Rankings
Forks count: 10.1%
Dependent repos count: 15.5%
Average: 19.1%
Stargazers count: 21.1%
Dependent packages count: 29.8%
Maintainers (1)
david.c.sterratt@ed.ac.uk
Last synced: 11 months ago

Dependencies

pkg/retistruct/DESCRIPTION cran
  • R >= 3.5.0 depends
  • R.matlab * imports
  • R6 * imports
  • RImageJROI * imports
  • RTriangle >= 1.6 imports
  • foreign * imports
  • geometry >= 0.4.3 imports
  • png * imports
  • rgl * imports
  • sp * imports
  • ttutils * imports
  • RGtk2 * suggests
  • cairoDevice * suggests
  • gWidgets2 >= 1.0.6 suggests
  • gWidgets2RGtk2 >= 1.0.6 suggests
  • spelling * suggests
  • testthat * suggests
pkg/retistructdemos/DESCRIPTION cran
  • retistruct >= 0.5.7 depends