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Auto-Bayes

Auto-Bayes is a software package based on Bayesian statistics and requires no user dependent parameters for molecule detection and image reconstruction for Single-Molecule Localization Microscopy (SMLM), including photoactivated localization microscope (PALM), stochastic optical reconstruction microscope (STORM), and direct stochastic optical reconstruction microscopy (dSTORM), etc.

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FOCAL

FOCAL (Fast Optimized Cluster Algorithm for Localizations) is a rapid density based algorithm for detecting clusters in localization microscopy datasets.

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WaveTracer

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Clus-Doc

Clus-Doc is a software that quantifies both the spatial distribution of a protein as well as its colocalization status. It may be used to quantify signaling activity and protein colocalization at the level of individual proteins.

irene's picture

SuReSim

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.

volker's picture

ThunderSTORM

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 PALM and STORM. Our philosophy in developing ThunderSTORM has been to offer an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data.

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Lama: The LocAlization Microscopy Analyzer

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.

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MosaicIA

Package/Library: 
Fiji
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SR-Tesseler

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.

volker's picture

FISH-quant

Workflow Language: 
MATLAB
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