A simple tool to correct chromatic shifts as well as temporal drift (including translations and rotations), based on spectral correlation.
building prefix tree from LIN codes
Icy is an open community platform for bioimage informatics
Block Mapping and Gathering with Entropy
Bio-Formats library patched for Icy.
The patch consist of replacing Apache Commons IO library by a newer version and also replacing org.json library with the custom version embedded into Micro-Manager to make it work properly.
This Icy bioimage analysis plugin was developped to help biologists detect late cytokinetic bridges on static immunofluorescence images.
The TensorFlow library manager plugin. This plugin allows users to choose the TF version to be used on runtime
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