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Open Source Science

https://github.com/biop/qupath-extension-abba

QuPath extension for Aligning Big Brains and Atlases

https://github.com/biop/qupath-extension-abba

Science Score: 39.0%

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
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

QuPath extension for Aligning Big Brains and Atlases

Basic Info
  • Host: GitHub
  • Owner: BIOP
  • License: mit
  • Language: Java
  • Default Branch: main
  • Size: 229 KB
Statistics
  • Stars: 6
  • Watchers: 3
  • Forks: 2
  • Open Issues: 7
  • Releases: 9
Created over 4 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

QuPath ABBA extension

This repo adds some support for the ABBA plugin in QuPath.

Installing

In QuPath 0.6, this extension should be installed via the QuPath BIOP catalog.

Don't forget to restart QuPath (but not your computer).

Citing

If you use ABBA in your work, please cite the paper below:

[!IMPORTANT] Chiaruttini, N.; Castoldi, C.; Requie, L. et al. ABBA+BraiAn, an integrated suite for whole-brain mapping, reveals brain-wide differences in immediate-early genes induction upon learning. Cell Reports (2025).\ https://doi.org/10.1016/j.celrep.2025.115876

Please do not forget to cite other tools you may use, such as DeepSlice, Brainglobe, QuPath...

Building

You can build the QuPath ABBA extension from source with

bash gradlew clean build

The output will be under build/libs.

  • clean removes anything old
  • build builds the QuPath extension as a .jar file and adds it to libs

Owner

  • Name: BioImaging And Optics Platform (BIOP)
  • Login: BIOP
  • Kind: organization
  • Location: Lausanne, Switzerland

All the code that is publicly available/published by the BioImaging And Optics Platform (BIOP)

GitHub Events

Total
  • Create event: 5
  • Issues event: 6
  • Release event: 4
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 30
  • Push event: 13
  • Pull request event: 7
Last Year
  • Create event: 5
  • Issues event: 6
  • Release event: 4
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 30
  • Push event: 13
  • Pull request event: 7

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 4
  • Total pull requests: 3
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.75
  • Average comments per pull request: 5.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 months
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 5.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • carlocastoldi (2)
  • NicoKiaru (2)
Pull Request Authors
  • carlocastoldi (6)
  • GuillaumeLeGoc (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

build.gradle maven
  • ch.epfl.biop:qupath-extension-warpy 0.2.1 implementation
  • commons-io:commons-io 2.11.0 implementation
  • io.github.qupath:qupath-gui-fx $qupathVersion implementation
  • net.imglib2:imglib2-realtransform 3.1.2 implementation
  • org.slf4j:slf4j-api 1.7.30 implementation
  • io.github.qupath:qupath-gui-fx $qupathVersion testImplementation
  • org.junit.jupiter:junit-jupiter-api 5.7.2 testImplementation
  • org.junit.jupiter:junit-jupiter-engine * testRuntimeOnly
.github/workflows/build_jar.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
  • actions/upload-artifact v2 composite
.github/workflows/gradle.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
.github/workflows/publish-release.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
.github/workflows/publish-snapshot.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite