Particle tracking software tools | Super resolution imaging analysis
Resolving the movement of individual molecules in living cells by single particle tracking methods has allowed many molecular behaviors to be deciphered over the past three decades. These methods have increasingly benefited from advances in microscopy of single nano-objects such as fluorescent dye molecules, proteins or nanoparticles as well as tiny absorbing metal nanoparticles. In parallel to these efforts aiming at tracking ever smaller and more photostable nano-objects in living cells, the development of localization-based super-resolution imaging provided means to increase the number of single molecules tracked on a single cell.
It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.
Tracks intra- and inter-cellular phenomena. TrackMate simplifies the export and exchange of data and results with other tracking tools and/or analysis applications. It is useful for a wide range of tracking applications, ranging from single-particle tracking of subcellular organelles to cell lineage analysis. This tool can detect foci beyond what the human eye can distinguish via the quality threshold parameter.
Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Restores images from microscopic data. Huygens is based on the deconvolution approach that reassigns out-of-focus light to its origin, thus improves signal-to-noise in images. It can use physically-acquired or simulated point-spread functions (PSFs) for characterization of optical system being deconvolved. The tool shows high-performance in in-house tests on deconvolution compared to other software packages. It provides intuitive wizards for parameter selection and processing.
Automates investigation related to dynamic microtubules within total internal reflection fluorescence (TIRF) images. MTrack is an ImageJ or Fiji plug-in that consists of two main components: the first one is able to generate trajectories by considering microtubules and their growing; the second one calculates population statistics and fits models of dynamic behavior by exploiting results from the first module.
Uses for fluorescence image analysis, visualization, simulation, and acquisition. SimFCS is a scientific software for data form spectroscopy and fluorescence microscopy. It can be applied to Fluorescence Correlation Spectroscopy, Fluorescence Lifetime Imaging, Pair correlation function, Image Mean Square Displacement, Single Particle and Modulation Tracking, Raster and Spatio-temporal Image Correlation Spectroscopy and many other.
A full set of MATLAB routines as a guide to localization image processing. These routines can be used to perform the image processing element of localization microscopy, and includes resolution analysis. Additional scripts are included to perform : image simulation for testbenching and validation ; batch processing of multiple files ; fiducial marker tracking and drift correction ; chromatic offset correction ; and molecular trajectory imaging.