Software breakthrough for super-resolution microscopy

 

Germany-based physicists have unveiled open source software to quickly and efficiently reconstruct images from super-resolution structured illumination microscopy data.

 

Super-resolution SIM is widely used to analyse dynamic processes in living cells, but the data obtained via this method demands complex mathematical image reconstruction to create a high resolution image.

 

Algorithms for such SIM reconstructions can be found in literature, but these are not easy to use and are either provided as proprietary components of commercial SIM microscopes or exist as purpose-written tools by different research groups.

 

What's more, various open-source solutions, such QuickPALM25 and rapidSTORM26 are now available for the related field of super-resolved localization microscopy.

 

With this is mind, Dr. Marcel Müller from the Biomolecular Photonics Group at University of Bielefeld, and colleagues, developed an easy-to-use plugin that provides reconstructions for a range of SIM platforms, directly within public domain Java-based image processing program software, ImageJ.

 

Called fairSIM - free analysis and interactive reconstruction for structured illumination microscopy - the plugin has been designed to provide single-slice reconstructions of SR-SIM systems working with two-beam and three-beam interference for pattern generation.

 

"It is based on the well-established SIM illumination technique... and the corresponding reconstruction algorithms," says Müller. "By combining multiple raw images, each acquired under structured illumination by a defined pattern, these algorithms allow to enhance the resolution twofold in comparison with the corresponding wide-field image."

 

Crucially, the plugin removes the hurdle of generating a complex implementation of a reconstruction algorithm.

 

 

Researchers have successfully tested fairSIM with different samples and microscopes, and as Müller says: "For the necessary post-processing, [researchers] no longer need to develop their own complicated solutions but can use our software directly."

 

"And, thanks to its open source availability, they can adjust [the plug-in] to fit their problems," he adds.

 

Research is published in Nature Communications.