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

An extension for QuPath with some tools made at the BIOP.

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

Science Score: 26.0%

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
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.4%) to scientific vocabulary

Keywords

qupath
Last synced: 6 months ago · JSON representation

Repository

An extension for QuPath with some tools made at the BIOP.

Basic Info
  • Host: GitHub
  • Owner: BIOP
  • License: apache-2.0
  • Language: Groovy
  • Default Branch: main
  • Homepage:
  • Size: 764 KB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 3
  • Open Issues: 0
  • Releases: 13
Topics
qupath
Created over 4 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

QuPath BIOP Extension

This repo adds some tools developed at the BIOP to ease scripting and assist user project in Qupath

[!WARNING] Versions from v3.3.0 or above of this extension will only work on QuPath 0.6.0 or later. Please update QuPath to the latest version. In case you are stuck with QuPath v0.5.1, the last release to work is v3.2.0

Installing

On QuPath 0.6.x

  • Install and setup the qupath-biop-catalog first.
  • Open the Extension Manager Extension -> Manage extensions
  • Follow steps described in the official documention to browse and install/update the latest version of QuPath BIOP extension from the QuPath BIOP catalog.

[!NOTE] If your extensions directory is unset, create a new empty folder somewhere on your computer. On QuPath, go under Edit -> Preferences -> Extensions and browse the empty folder you've just created. Extensions will then be added inside this folder.

  • You might then need to restart QuPath (but not your computer).

On QuPath 0.5.x

Download the latest qupath-extension-biop-[version].jar file from releases and drag it onto the main QuPath window.

If you haven't installed any extensions before, you'll be prompted to select a QuPath user directory. The extension will then be copied to a location inside that directory.

You might then need to restart QuPath (but not your computer).

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
  • Release event: 4
  • Issues event: 3
  • Issue comment event: 2
  • Push event: 6
Last Year
  • Create event: 5
  • Release event: 4
  • Issues event: 3
  • Issue comment event: 2
  • Push event: 6

Dependencies

.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
build.gradle maven
  • com.google.code.gson:gson 2.8.8 implementation
  • net.imglib2:imglib2-realtransform 3.1.1 implementation
  • org.junit.jupiter:junit-jupiter-api 5.7.2 testImplementation
  • org.junit.jupiter:junit-jupiter-engine * testRuntimeOnly