Super-resolution microscopy

Synonyms
palm
Photoactivated localization microscopy

Fourier Ring Correlation

Description

Calculate the Fourier ring correlation (FRC). The FRC can be used as a resolution criterion for super resolution microscopy. The Plugin can display a plot of the FRC curve, along with the LOESS smoothed version of the curve. Finally it displays the threshold method used and the intersection of the FRC with the threshold, providing the FIRE number. It can be used on two open images or on pairs of images in batch mode. 2654 2655

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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

Drift correction using PALMsiever

Description

Two workflows are proposed here:

one based on fiducials, the other one on cross-correlation.

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RapidSTORM

Description

The rapidSTORM project is an open source evaluation tool that provides fast and highly configurable data processing for single-molecule localization microscopy such as dSTORM. It provides both two-dimensional and three-dimensional, multi-color data analysis as well as a wide range of filtering and image generation capabilities. The general operation of rapidSTORM is described in Wolter et al (2012).

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Huygens

Description

The Huygens Software Suite consists of different image processing packages with functionalities that include deconvolution, interactive analysis, and volume visualization of 2D-3D multi-channel and time series images from fluorescence microscopes such as widefield, confocal, multi-photon, spinning disk, Array Detector, STED, and Light Sheet

PALMsiever

Description

PALMsiever is a MATLAB-based application that allows the filtering (sieving) and analysis of localization-microscopy data. It provides the ability to render the data using different visualization algorithms and perform simple measurements on the point-localization data. It is extensible using simple MATLAB scripts and a number of plugins is already provided with the software itself, including a clustering algorithm and 3D rendering 2496. Strengths: intuitive, easy navigation through the point-localization data Limitations: no multi-color

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