fiji-plugin

hadim/maskflow

Maskflow: Object Detection and Segmentation for Cell Biology.

hilaprat/evm-imagej2

phflot/variational_aligner_IJ

ImageJ and Fiji Plugin for fast, variational 1D alignment of multichannel linescan data

sedflix/EmbryoSegmentation

An ImageJ PlugIn for cell segmentation in an embryo of c.elegans

Turku-BioImaging/ColonyArea

ImageJ-plugin that performs standard analysis of colony formation assays conducted in 6- to 24-well dishes.

acayuelalopez/MitochondrialAnalyzer_

This is a Java-based plugin for quantification of mitochondrial characteristics and subsequent morphology operational under either ImageJ or Fiji.

antinos/T-SNE-ImageJ

An ImageJ/Fiji port of Leif Jonsson's pure Java t-SNE (https://github.com/lejon/T-SNE-Java)

BenjaminEscribano/PrairieDataManager

Prairie 2-Photon Microscopy Data Manager for recursive batch processing ans analysis with Fiji

CellMoTher/AccPbFRET

An ImageJ plugin for analysis of acceptor photobleaching FRET images :electric_plug:

CellMoTher/RiFRET

An ImageJ plugin for intensity-based three-filter set (ratiometric) FRET :electric_plug:

h39s/VessCoopJ

ImageJ Plugin for Automated Cancer Cell Vessel Co-option Analysis

karlvosatka/analyze_blebs

Analyze_Blebs is a semi-automated ImageJ/FIJI-based plugin for analysis of blebbing cells designed for users at all experience levels and blebs of all types.

MichaelWrana/MicroscopePlugins

sankeert1999/Virtual-Orientation-Tools-VOTj

Virtual Orientation Tool FIJI (VOTj) : A Fiji plugin for object centering and alignment

xulman-obsoleteProjects/image-net-transfers-java

Java implementation of a proprietary image transfer protocol

ComputationalIntelligenceGroup/MaxLoGs

Maximum of Laplacian of Gaussian filters (imageJ plugin)

ComputationalIntelligenceGroup/ObjCounter

ObjCounter ImageJ plugin for object segmentation and counting

ekatrukha/AveragingND

FIJI plugin for the averaging of ND (2/3/4D) images

hansenjn/ExtractSharpestPlane_JNH

ExtractSharpestPlane_JNH is an ImageJ/FIJI plugin to automatically extract the sharpest plane by highest SD from image stacks for large data sets.

hansenjn/NuclQ

NuclQ - an ImageJ plugin to quantify intensity levels by distance to the nuclear membrane.

nurlicht/CellulyzerDemo

Automated tracking and interactive visualization/simulation of select cellular processes

sufyanshk/imagej

ImageJ macros and plugins.

thorstenwagner/ij-irregular-watershed

Watershed for irregular objects