Abstract
Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses.
Highlights
Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy
The improvement in spatial resolution achieved in superresolved structured illumination fluorescence microscopy (SR-SIM) is accomplished by illuminating a sample with a well-defined set of sinusoidal illumination intensity patterns, that is, typically a set of interference patterns[1]
FairSIM is implemented as Java plugin, so it allows to carry out SR-SIM reconstructions directly from within ImageJ/Fiji
Summary
Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. The light modulation leads to frequency mixing between the harmonic pattern frequency and the sample frequencies, which is demodulated by a digital image reconstruction step[2] This enables access to previously unobservable high-frequency components, and improves spatial resolution. SIM data sets are usually acquired by a modified wide-field microscope, where a light-modulating component is introduced into the excitation path. Various well-known open-source solutions, for example, QuickPALM25 and rapidSTORM26, with different feature sets (a summary of which was published recently27), and often direct integration with ImageJ, are available for data analysis
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