https://github.com/fmi-faim/fmi-ij2-plugins

A collection of ImageJ2 plugins for use with KNIME
https://github.com/fmi-faim/fmi-ij2-plugins

bio-image-analysis image-processing imagej knime

Last synced: 10 days ago
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A collection of ImageJ2 plugins for use with KNIME

• Host: GitHub
• URL: https://github.com/fmi-faim/fmi-ij2-plugins
• Owner: fmi-faim
• License: lgpl-3.0
• Created: 2016-10-27T08:20:08.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2024-05-02T11:03:25.000Z (over 1 year ago)
• Last Synced: 2024-05-02T21:13:25.968Z (over 1 year ago)
• Topics: bio-image-analysis, image-processing, imagej, knime
• Language: Java
• Homepage:
• Size: 187 KB
• Stars: 7
• Watchers: 2
• Forks: 3
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
# fmi-ij2-plugins

[![NodePit](https://img.shields.io/badge/NodePit-FMI%20KNIME%20Plugins-yellow.svg)](https://nodepit.com/iu/ch.fmi.knime.plugins)

[![GitHub Release](https://img.shields.io/github/release/fmi-faim/fmi-ij2-plugins.svg)](https://github.com/fmi-faim/fmi-ij2-plugins/releases)

[![Build Status](https://github.com/fmi-faim/fmi-ij2-plugins/actions/workflows/build-main.yml/badge.svg)](https://github.com/fmi-faim/fmi-ij2-plugins/actions/workflows/build-main.yml)

[![Codacy Badge](https://app.codacy.com/project/badge/Grade/97b75dbd7ff241888fb2339fdb5dcebc)](https://www.codacy.com/gh/fmi-faim/fmi-ij2-plugins/dashboard?utm_source=github.com&utm_medium=referral&utm_content=fmi-faim/fmi-ij2-plugins&utm_campaign=Badge_Grade)

[![DOI](https://zenodo.org/badge/72086675.svg)](https://zenodo.org/badge/latestdoi/72086675)

## Installation in KNIME

To use these plugins in KNIME, please activate the update site `https://community.knime.org/download/ch.fmi.knime.plugins.update/` as well as the [KNIME Image Processing Nightly Builds](https://www.knime.com/wiki/knime-image-processing-nightly-build).

## Manual installation in KNIME

If you want to install this plugin manually via the KNIME ImageJ2 integration, you'll have to install the `fmi-ij2-plugins` jar file as well as all the dependencies listed below.

1. Install `fmi-ij2-plugins.jar` from the [latest release](https://github.com/fmi-faim/fmi-ij2-plugins/releases/latest) via *File > Preferences* into *KNIME > Image Processing Plugin > ImageJ2 Plugin Installation*.

2. The following additional files (dependencies) are required:

| Project | Download `jar` from maven.imagej.net |

| --- | --- |

| [`AnalyzeSkeleton_`](https://github.com/fiji/AnalyzeSkeleton/) | [`AnalyzeSkeleton_-3.4.2.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/AnalyzeSkeleton_/3.4.2/AnalyzeSkeleton_-3.4.2.jar) |

| [`Descriptor_based_registration`](https://github.com/fiji/Descriptor_based_registration) | [`Descriptor_based_registration-2.1.7.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/Descriptor_based_registration/2.1.7/Descriptor_based_registration-2.1.7.jar) |

| [`Fiji_Plugins`](https://github.com/fiji/Fiji_Plugins) | [`Fiji_Plugins-3.1.1.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/Fiji_Plugins/3.1.1/Fiji_Plugins-3.1.1.jar) |

| [`fmi-trackmate-addons`](https://github.com/fmi-faim/fmi-trackmate-addons) | [`fmi-trackmate-addons-0.1.2.jar`](http://maven.imagej.net/service/local/repositories/releases/content/ch/fmi/fmi-trackmate-addons/0.1.2/fmi-trackmate-addons-0.1.2.jar) |

| [`guava`](https://github.com/google/guava) | [`guava-21.0.jar`](http://maven.imagej.net/service/local/repositories/central/content/com/google/guava/guava/21.0/guava-21.0.jar) |

| `jdom2` | [`jdom2-2.0.6.jar`](http://maven.imagej.net/service/local/repositories/bedatadriven/content/org/jdom/jdom2/2.0.6/jdom2-2.0.6.jar) |

| [`jgrapht-core`](https://github.com/jgrapht/jgrapht) | [`jgrapht-core-1.4.0.jar`](http://maven.imagej.net/service/local/repositories/central/content/org/jgrapht/jgrapht-core/1.4.0/jgrapht-core-1.4.0.jar) |

| [`jts-core`](https://github.com/locationtech/jts) | [`jts-core-1.18.1.jar`](https://repo.maven.apache.org/maven2/org/locationtech/jts/jts-core/1.18.1/jts-core-1.18.1.jar) |

| [`legacy-imglib1`](https://github.com/fiji/legacy-imglib1) | [`legacy-imglib1-1.1.9.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/legacy-imglib1/1.1.9/legacy-imglib1-1.1.9.jar) |

| [`mpicbg`](https://github.com/axtimwalde/mpicbg/tree/master/mpicbg) | [`mpicbg-1.4.1.jar`](http://maven.imagej.net/service/local/repositories/releases/content/mpicbg/mpicbg/1.4.1/mpicbg-1.4.1.jar) |

| [`SPIM_Registration`](https://github.com/fiji/SPIM_Registration) | [`SPIM_Registration-5.0.21.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/SPIM_Registration/5.0.21/SPIM_Registration-5.0.21.jar) |

| [`TrackMate_`](https://github.com/fiji/TrackMate) | [`TrackMate_-6.0.1.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/TrackMate_/6.0.1/TrackMate_-6.0.1.jar) |

| [`TrackMate_extras`](https://github.com/tinevez/TrackMate-extras) | [`TrackMate_extras-0.0.4.jar`](http://maven.imagej.net/service/local/repositories/releases/content/org/scijava/TrackMate_extras/0.0.4/TrackMate_extras-0.0.4.jar) |