Image reconstruction software tools | Super resolution imaging analysis
Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms.
Provides a complete set of tools for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy (SMLM) methods. ThunderSTORM is a program that offers many different processing and post-processing methods so that users can adapt the analysis to their data. It is able to process the data using any combination of the implemented feature enhancing, spot detection and fitting methods.
A set of programs to aid in the acquisition and image analysis of data in “photoactivated localization microscopy” (PALM) and “stochastic optical reconstruction microscopy” (STORM). QuickPALM provides a complete solution for acquisition, reconstruction and visualization of 3D PALM or STORM images, achieving resolutions of ~40 nm in real time. This software package should greatly facilitate the conversion of many laser-excitation widefield or TIRF microscopes into powerful super-resolution microscopes.
Enables online image processing essential for high-throughput nanoscopy. WindSTORM is an online application for high-density emitter localization that uses non-iterative linear deconvolution to decompose overlapping emitters and retrieve their precise locations. It achieves real-time image processing on a GPU device and maintains high accuracy and fidelity even in the presence of high non-uniform background in various biological samples.
Assists in the creation and visualization of 3D fluorescence volume rendering. MicroSCoBioJ contains three plugins: (1) Mesh Maker MicroSCoBioJ that computes the triangles or tetrahedra mesh corresponding to an user-defined treshold; (2) Mesh Viewer MicroSCoBioJ that shows up to four different meshes and displays the mesh as points, lines, or fill surface; and (3) WAT MicroSCoBioJ Weight Adaptive Threshold.
Provides a user-friendly means of visualizing, filtering and analyzing localization microscopy (LM) data. PALMsiever includes drift correction, clustering, intelligent line profiles, many rendering algorithms, and 3D data visualization. It incorporates the main analysis and data processing modalities used by experts in the field, as well as several new features we developed, and makes them broadly accessible. It can easily be extended via plugins and is provided as free of charge open-source software.
Analyzes high-density 2D STORM data using compressed sensing. For an experimental data set with varying emitter density, L1H analysis is ~300-fold faster than interior point methods. This drastic reduction in computational time should allow the compressed sensing approach to be routinely applied to super-resolution image analysis.
An interactive open-source software with a graphical user interface, which allows performing processing steps for localization data in an integrated manner. This includes common features and new tools such as correction of chromatic aberrations, drift correction based on iterative cross-correlation calculations, selection of localization events, reconstruction of 2D and 3D datasets in different representations, estimation of resolution by Fourier ring correlation, clustering analysis based on Voronoi diagrams and Ripley’s functions. SharpViSu is optimized to work with eventlist tables exported from most popular localization software. The functionality of SharpViSu is extendable via plugins, such as ClusterViSu for comprehensive cluster analysis of localization microscopy data. It includes tools such as calculations of Voronoi and Ripley statistics with Monte-Carlo simulations, different modes of reconstruction (e.g. based on Gaussian blur or Ripley’s functions) and segmentation of density maps, retrieval of geometrical properties of detected clusters, segmentation based on Voronoi tessellation.