FlyLimbTracker

Bio Image Analyst
Developper

  FlyLimbTracker is  a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving Drosophila flies. This approach can be used to measure leg segment motions during a variety of locomotor and grooming behaviors.

For now the plugin have to be downlaoded directly from the EPFL website (see link), not from the search bar as usual in ICY.

 

NeuriteTracer

Bio Image Analyst

"The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length."[...]" NeuriteTracer is a fast simple-to-use ImageJ plugin for the analysis of outgrowth in two-dimensional fluorescence microscopy images of neuronal cultures. The plugin performed well on images from three different types of neurons with distinct morphologies."

AVEMAP

Bio Image Analyst

Measures wound-healing assay videos, 

 For each video, the velocity and the order parameter are analyzed in time and space to extract quantitative parameters characterizing the cell motility phenotype. The different conditions (videos) can then be classified according to these parameters.

QuimP

Bio Image Analyst
Developper

Summary

QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane. QuimP's unique selling point is the possibility to aggregate data from many cells in form of spatio-temporal maps of dynamic events, independently of cell size and shape. QuimP has been successfully applied to address a wide range of problems related to cell movement in many different cell types. 

Introduction

Angiogenesis / Sprout Analyzer

Bio Image Analyst
Developper

The Sprout Morphology plugin measures sprout number, length, width and cell density of endothelial cell (EC) sprouts grown in a bead sprouting assay. It optionally includes measuring the coverage of these sprouts with pericytes included in the assay, as well as the endothelial cell/pericyte ratio.

SOAX

Bio Image Analyst
Developper

SOAX is an open source software tool to extract the centerlines, junctions and filament lengths of biopolymer networks in 2D and 3D images. It facilitates quantitative, reproducible and objective analysis of the image data. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments.