Icy Spot Tracking

Description

Up to version 2 it was known as the ‘Probabilistic particle tracker’ plugin.

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Analysis of Microtubule Orientation: Tracking with ImageJ, Directionality Analysis with Matlab

Bioimage Analyst
Developer

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

Bioimage Analyst
Developer

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

Bioimage Analyst
Developer

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.

PTA2

Description

"PTA2 is an ImageJ1.x plugins that enable automatic particle tracking"

This plugin is developed specifically for single-molecule imaging, so it's good at tracking spots with noisy background. 

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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. 

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Tracking2.0

Description

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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MosaicSuite

Description

Image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy. Tools included:

  • 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time.
  • Optimal filament segmentation of 2D images. 
  • Curvature filters for image filtering, denoising, and restoration. 
  • Image naturalization for image enhancement based on gradient statistics of natural-scence images. 
  • Tool for automatically send and distribute jobs on clusters and get back the results.
  • Multi-region image segmentation of 2D and 3D images without needing to know the number of regions beforehand. 
  • Squassh for globally optimal segmentation of piecewise constant regions in 2D and 3D images and for object-based co-localization analysis. 
  • Tool for inferring spatial interactions between patterns of objects in images or between coordinates read from a file.
  • Tool for robust, histogram-based background subtraction well suited to correct for inhomogeneous illumination artifacts.
  • A tool to estimate the Point-Spread Function of the microscopy out of 2D fluorescence images.
  • A tool to measure the 3D Point-Spread Function of a confocal microscope from an image stack.
  • Addition of synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. 
  • Convolution of an image with a Bessel function in order to simulate imaging with a microscope. 
  • A utility to detect bright spots in images and estimate their center. 
  • A utility to create manual segmentations to be used as ground truth to test and benchmark automatic segmentation algorithms.
  • A tool for replacing one color in an image with another color.
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