Synonyms
SMLM
STORM
Direct stochastic optical reconstruction microscopy
GSDIM
PALM
Photoactivated Localization Microscopy
Fluorescence Photoactivation Localization Microscopy
Ground State Depletion Individual Molecule Return
dSTORM
Stochastic optical reconstruction microscopy

FandPLimitTool

Description

Software for computing single molecule localization accuracies and resolution measures

The FandPLimitTool is a GUI based software module that allows users to calculate the limits to the accuracy with which parameters can be estimated from single molecule imaging data. The software supports calculation of limits for the 2D/3D location estimation problem and the 2D/3D distance-estimation/resolution problem. The location estimation problem is concerned with the task of determining the position of a single molecule and the distance-estimation/resolution problem is concerned with the task of determining the distance of separation between two single molecules. The user can calculate limits for a variety of imaging scenarios.

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SQUIRREL

Description

NanoJ-SQUIRREL (Super-resolution Quantitative Image Rating and Reporting of Error Locations) is a software package designed for assessing and mapping errors and artefacts within super-resolution images. This is achieved through quantitative comparison with a reference image of the same structure (typically a widefield, TIRF or confocal image). SQUIRREL produces quantitative maps of image quality and resolution as well as global image quality metrics.

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SQUIRREL

2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals.

Description

This script includes a rough feature detection and then fine 2D Gaussian algorithm to fit Gaussians within detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by linearising the equation. This implementation is for isotropic (spherical) or anistropic (longer in x/y) diagonally covariant Gaussians but not fully covariant Gaussians (anisotropic and rotated). 

3D-DAOSTORM

Description

Stochastic optical reconstruction microscopy (STORM) and related methods achieves sub-diffraction-limit image resolution through sequential activation and localization of individual fluorophores. The analysis of image data from these methods has typically been confined to the sparse activation regime where the density of activated fluorophores is sufficiently low such that there is minimal overlap between the images of adjacent emitters. Recently several methods have been reported for analyzing higher density data, allowing partial overlap between adjacent emitters. However, these methods have so far been limited to two-dimensional imaging, in which the point spread function (PSF) of each emitter is assumed to be identical.

In this work, we present a method to analyze high-density super-resolution data in three dimensions, where the images of individual fluorophores not only overlap, but also have varying PSFs that depend on the z positions of the fluorophores.

 

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THOT

Description

Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

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thot

SuReSim

Description

SuReSim (Super Resolution Simulation) is an open-source simulation software for Single Molecule Localization Microscopy (SMLM). The workflow of the SuReSim algorithm starts from a ground truth structure and lets the user choose to either directly simulate 3D localizations or to create simulated *.tiff-stacks that the user can analyze with any given SMLM reconstruction software. A 3D structure of any geometry, either taken from electron microscopy, designed de-novo from assumptions or known structural facts, is fluorophore-labeled in silico. A defined set of parameters is used to calculate and visualize the 3D localizations of the corresponding labels. The software package is accompanied with a library of model structures that can be imported and simulated. Users manual with tutorial provided.

SureSim screenshot

Lama: The LocAlization Microscopy Analyzer

Description

LocAlization Microscopy Analyzer (LAMA) is a software tool that contains several well-established data post processing algorithms for single-molecule localization microscopy (SMLM) data. LAMA has implemented algorithms for cluster analysis, colocalization analysis, localization precision estimation and image registration. LAMA works with a graphical user interface (GUI), and accepts simple input data formats as supported by various single- molecule localization software tools.

SR-Tesseler

Description

Localization-based super-resolution techniques open the door to unprecedented analysis of molecular organization. This task often involves complex image processing adapted to the specific topology and quality of the image to be analyzed. SR-Tesseler is an open-source segmentation software using Voronoï tessellation constructed from the coordinates of localized molecules. It allows precise, robust and automatic quantification of protein organization at different scales, from the cellular level down to clusters of a few fluorescent markers. SR-Tesseler is insensitive to cell shape, molecular organization, background and noise, allowing comparing efficiently different biological conditions in a non-biased manner, and perform quantifications on various proteins and cell types. SR-Tesseler software comes with a very simple and intuitive graphical user interface, providing direct visual feedback of the results and is freely available under GPLv3 license.

Density map of a neuron extracted from the Voronoï diagram

GDSC Single Molecule Localisation Microscopy

Description

The GDSC Single Molecule Light Microscopy (SMLM) plugins is a package of tools for single molecule localisation analysis. - Fitting Plugins: get point cloud from super resolution image. - Results Plugins: organize results. - Analysis plugins - Model plugins

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DBSCAN clustering using PALMsiever

Description

DBSCAN (Density-based spatial clustering of applications with noise) performs multi-dimensional clustering based on the local density of points. This plugin is implemented for 2-3 dimensions.

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