OligoMacro Toolset

Description

OligoMacro Toolset, is an ImageJ macro-toolset aimed at isolating oligodendrocytes from wide-field images, tracking isolated cells, characterizing processes morphology along time, outputting numerical data and plotting them. It takes benefit of ImageJ built-in functions to process images and extract data, and relies on the R software in order to generate graphs.

need a thumbnail

Simple-Tracker

Description

SIMPLETRACKER a simple particle tracking algorithm that can deal with gaps.

Tracking , or particle linking, consist in re-building the trajectories of one or several particles as they move along time. Their position is reported at each frame, but their identity is yet unknown: we do not know what particle in one frame corresponding to a particle in the previous frame. Tracking algorithms aim at providing a solution for this problem. 

simpletracker.m is - as the name says - a simple implementation of a tracking algorithm, that can deal with gaps. A gap happens when one particle that was detected in one frame is not detected in the subsequent one. If not dealt with, this generates a track break, or a gap, in the frame where the particle disappear, and a false new track in the frame where it re-appear. 

need a thumbnail

@msdanalyzer

Description

Mean square displacement (MSD) analysis is a technique commonly used in colloidal studies and biophysics to determine what is the mode of displacement of particles followed over time. In particular, it can help determine whether the particle is:

  • freely diffusing;
  • transported;
  • bound and limited in its movement.

On top of this, it can also derive an estimate of the parameters of the movement, such as the diffusion coefficient.

@msdanalyzer is a MATLAB per-value class that helps performing this kind of analysis. The user provides several trajectories he measured, and the class can derive meaningful quantities for the determination of the movement modality, assuming that all particles follow the same movement model and sample the same environment.

has function
Examples of tracks to perform MSD analysis.

MaMuT

Description

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

Particle Tracker 2D/3D

Description

Easy-to-use, computationally efficient, two- and three-dimensional, feature point-tracking tool for the automated detection and analysis of particle trajectories as recorded by video imaging in cell biology. 


The tracking process requires no apriori mathematical modelling of the motion, it is self-initialising, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. 


The plugin is well suited for video imaging in cell biology relying on low-intensity fluorescence microscopy. It allows the user to visualize and analyze the detected particles and found trajectories in various ways:

  • Preview and save detected particles for separate analysis
  • Global non progressive view on all trajectories
  • Focused progressive view on individually selected trajectory
  • Focused progressive view on trajectories in an area of interest

It also allows the user to find trajectories from uploaded particles position and information text files and then to plot particles parameters vs. time - along a trajectory

CellTracker

Description

CellTracker software is a platform for tracking nuclear and cytoplasmic fluorescence intensities from live cell microscopy time series data.

 

Requires visual C++

Track Processor Instant Speed

Description

This display the Instant Speed of tracks for the Icy Track Manager.

StackReg

Description

This plugin registers (= aligns, matches) a stack of image slices.

Manual Tracking ImageJ

Description

An ImageJ plugin for manually tracking objects by mouse clicking. 

This plugin is bundled with Fiji. 

 

has function