"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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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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A set of classes and functions which can be used by plugins performing spot detection and spot tracking.

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