Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ

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.

Optimal 2D-SIM reconstruction by two filtering steps with Richardson-Lucy deconvolution

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Morphology and force probing of primary murine liver sinusoidal endothelial cells

“…In most of the publications, the structure of fenestrations in LSECs was described in fixed cells using electron microscopy, atomic force microscopy (AFM) or recently super‐resolution optical microscopy . However, in fixed (especially fixed‐dried) cells, the structure of fenestrations might be altered .…”

Tracking Fenestrae Dynamics in Live Murine Liver Sinusoidal Endothelial Cells

“…Last year our team reported that the quantitative imaging (QI) mode of atomic force microscopy (AFM) allowed the relatively fast and high‐resolution dynamic imaging of fenestrae in cultured LSECs . Moreover, high‐resolution three‐dimensional (3‐D) imaging of fenestrae on fixed LSECs using superresolution fluorescence microscopy recently became possible, indicating the future potential to investigate live LSECs under relevant physiological conditions . Those two Nobel Prize–awarded imaging technologies illustrate the impact of microscopy technology development on revealing new insights in LSEC biology and fenestrae.…”