ABSTRACT
UNLABELLED: SIMToolbox is an open-source, modular set of functions for MATLAB equipped with a user-friendly graphical interface and designed for processing two-dimensional and three-dimensional data acquired by structured illumination microscopy (SIM). Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination. AVAILABILITY AND IMPLEMENTATION: SIMToolbox, example data and the online documentation are freely accessible at http://mmtg.fel.cvut.cz/SIMToolbox. CONTACT: ghagen@uccs.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Actin Cytoskeleton/ultrastructure , Fluorescence , Lighting/methods , Microscopy, Fluorescence/methods , Software , Hep G2 Cells , Humans , Image Processing, Computer-Assisted , Imaging, Three-Dimensional/methodsABSTRACT
UNLABELLED: ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy. ThunderSTORM offers an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data. ThunderSTORM also offers a set of tools for creation of simulated data and quantitative performance evaluation of localization algorithms using Monte Carlo simulations. AVAILABILITY AND IMPLEMENTATION: ThunderSTORM and the online documentation are both freely accessible at https://code.google.com/p/thunder-storm/.
Subject(s)
Computer Graphics , Image Processing, Computer-Assisted/methods , Microscopy/methods , Software , Algorithms , Microscopy, Fluorescence/methods , Monte Carlo MethodABSTRACT
We introduce and demonstrate a new high performance image reconstruction method for super-resolution structured illumination microscopy based on maximum a posteriori probability estimation (MAP-SIM). Imaging performance is demonstrated on a variety of fluorescent samples of different thickness, labeling density and noise levels. The method provides good suppression of out of focus light, improves spatial resolution, and allows reconstruction of both 2D and 3D images of cells even in the case of weak signals. The method can be used to process both optical sectioning and super-resolution structured illumination microscopy data to create high quality super-resolution images.
Subject(s)
Algorithms , Imaging, Three-Dimensional , Lighting , Microscopy/methods , Probability , Animals , Cattle , Drosophila melanogaster/cytology , Fluorescence , Hep G2 Cells , Humans , Pollen/cytology , Signal-To-Noise RatioABSTRACT
Single-molecule localization microscopy methods offer high spatial resolution, but they are not always suitable for live cell imaging due to limited temporal resolution. One strategy is to increase the density of photoactivated molecules present in each image, however suitable analysis algorithms for such data are still lacking. We present 3denseSTORM, a new algorithm for localization microscopy which is able to recover 2D or 3D super-resolution images from a sequence of diffraction limited images with high densities of photoactivated molecules. The algorithm is based on sparse support recovery and uses a Poisson noise model, which becomes critical in low-light conditions. For 3D data reconstruction we use the astigmatism and biplane imaging methods. We derive the theoretical resolution limits of the method and show examples of image reconstructions in simulations and in real 2D and 3D biological samples. The method is suitable for fast image acquisition in densely labeled samples and helps facilitate live cell studies with single molecule localization microscopy.
