Object tracking




Fiji plugin for detecting, tracking and quantifying filopodia

EB1 tracking with Matlab

Submitted by Perrine on Mon, 04/08/2019 - 11:05

This module follow EB1 tracking with IJ. In this session, we will visualize the tracking results and also cover typical analysis protocols for the quantitative analysis of movement. Two dynamic numerical features could be extracted from tracking results: speed and direction. Estimation of movement speed from multiple trajectories is a popular indicator of movement, and we will quickly go over the method for estimating the average speed of EB1 movement along microtubule. Movement direction is another quantitative feature, but is rarely explored.

EB1 tracking with IJ

Submitted by Perrine on Mon, 04/08/2019 - 11:00

We take an example image data of microtubule binding protein EB1, and will study how to automatically track those signals and how to analyze the tracking results. We use ImageJ for measuring the temporal changes in signal positions, and will feed the tracking results for analyzing their dynamics using Matlab in the following session EB1 tracking with Matlab.

Nuclei Tracking (ImageJ)

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Manual tracking with TrackMate


Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji). 

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This method was originally designed to track objects (not necessarily spots) already identified in 2D 
frames and has been applied previously to particle tracking and analysis in high-speed atomic force microscopy image series.


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HyphaTracker Workflow

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.




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.

kymograph generation


Kymograph generation under ImageJ:

one simple solution, plot a line (ROI line) on the first frame, where you want to generate the kymograph.


Image  / Stacks  / Reslice

It will generate a new image were Y dimension is the time, and X the position on the line you have drawn.

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