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BioImageXD
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.
SuReSim / Super Resolution Simulation
A software tool that simulates localization data of arbitrary three-dimensional structures represented by ground truth models, allowing users to systematically explore how changing experimental parameters can affect potential imaging outcomes. SuReSim can generate simulated localizations from ground truth models in two alternative modes. Direct simulation (left) provides instant 3D visualization, allowing one to explore a structure and predict whether it can be resolved with SMLM. Furthermore, localization files and rendered images can be used for postprocessing of the data. The indirect approach (right) produces raw SMLM data in the form of image stacks. These can be analyzed with any SMLM reconstruction software. The reconstructed data can also be compared to ground truth data to validate the reconstruction software.
SMeagol
Generates highly realistic single molecule microscopy time-lapse image series aimed primarily at single particle tracking applications. The purpose of SMeagol is to enable realistic comparisons between the output of advanced analysis methods and known ground truth. SMeagol includes an extended MesoRD version for simulation of 3D diffusion in cellular compartments, diffusion limited reaction kinetics, surface adsorption, reactions in membranes and other complex aspects of reaction diffusion kinetics that do occur in cells, but are not considered in SPT analysis algorithms. In addition to the molecules’ trajectories, SMeagol integrates the 3D point spread function of the microscope, the kinetics of photo-activation, blinking and bleaching of the simulated fluorophores, background noise and camera specific parameters.
SOFI Simulation Tool / Super-resolution Optical Fluctuation Imaging Simulation toolbox
Models the imaging procedure of super-resolution optical fluctuation imaging. SOFI Simulation Tool incorporates SOFI and bSOFI algorithms, as well as a basic STORM algorithm consisting of segmentation of each frame and subsequent localization of single molecules using Gaussian fitting methods. The software generates simulated image stacks and calculates SOFI and STORM super-resolution images. It permits users to test numerous image acquisition settings prior to experimental work.
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