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Icy is an open community platform for bioimage informatics

A simple tool to correct chromatic shifts as well as temporal drift (including translations and rotations), based on spectral correlation.

Building a multiple sequence alignment well-suited for phylogenetic analysis from read mapping data

imglib2-icy ImgLib2 wrappers for Icy.

Local z-projection via the determination of a plane of reference.

A Fiji tool to detect, track and analyze cell-to-cell contacts.

First reported in Samassa et al., 2020, "Shigella impairs human T lymphocyte responsiveness by hijacking actin cytoskeleton dynamics and TCR vesicular trafficking"

Tools to measure tracking performance with the ISBI Challenge on Single-Particle Tracking metrics.

I adapted and copied code from by N. Chenouard, F. De Chaumon and S. Dallongeville so that it can run in batch and without Icy.

Estimating a confidence value at each branch of a phylogenetic tree from a matrix of pairwise evolutionary distances

Minimum Spanning Tree-based clustering

Extracting a nucleotide segment from a FASTA-formatted file

Translating the maximum number of codons using the minimum number of ORFs

Fast trimming of sequencing reads

Fast removal of contaminating reads from FASTQ file(s)

The TensorFlow library manager plugin. This plugin allows users to choose the TF version to be used on runtime

This Icy bioimage analysis plugin was developped to help biologists detect late cytokinetic bridges on static immunofluorescence images.

Spot Tracking plugin for Icy

Provides 3D vector mathematics classes.

Template to create new Icy plugin (POM file and base plugin class)