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.
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.
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.
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.
An open source, real-time data analysis and rendering tool for super-resolution imaging techniques that are based on single molecule detection and localization (e.g. stochastic optical reconstruction microscopy - STORM and photoactivation localization microscopy – PALM). GraspJ is an ImageJ plug-in with a convenient user interface, that allows high accuracy localization of single molecules as well as processing and rendering of high resolution images in real-time. GraspJ includes several features such as drift correction, multi-color, 3D analysis/rendering, and is compatible with a large range of data acquisition software. In addition, it allows easy interfacing with other image processing tools available with ImageJ.
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.
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.
Assists in reconstructing dense localization microscopy datasets. B-recs is an application that builds back super-resolution images at intermediate densities of active fluorophores. The theoretical limit for accurate reconstruction is one fluorophore per pixel on the camera, at higher densities, the accuracy quickly drops. Two options are offered to run this method: fiji plugin and command line tool.