Multifocal Structured Illumination Microscopy
Saturated Structured Illumination
Instant linear structured Illumination Microscopy

Quantification of outer ring diameters of centriole or PCM proteins of cycling HeLa cells in interphase


This workflow can be ran with data from 3D-SIM showing the centrosomes in order to compare the distribution of diameters of rings (or toroids) of different proteins from the centrioles or the peri centriolar material. It aims to reproduce the results of the Nature Cell Biology Paper Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material  from the same data set but with a different analysis method.

It is slightly different from the methods described in the paper itself, where the method was to work on a maximum intensity projection of a 3D-SIM stack, and then to fit circle to the centrioles to estimate the diameters of the toroids.

In this workflow, the images are read from the IDR , then process by thresholding (Maximum entropy auto thresholding with Image J), and processed by Analyze Particles  with different measurement sets, including the bouding box. Then the analysis of diameters and the statistical test are performed using R. All the code and data sets are available, and in the case of this paper have shown a layered organisation of the proteins.

Combined view from Figure 1 Lawo et al.



an open source ImageJ plugin suite for super-resolution structured illumination microscopy data quality control

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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. 2662

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SGP-dec, A Scaled Gradient Projection method for 2D and 3D images deconvolution


A deconvolution component applicable to confocal and STED microscopy. The MATLAB function fo this package implements the SGP method for n-dimensional object deblurring with the option of boundary effects removal. Although this is a preliminary version, results seem to be good from their paper (Zanella et al 2013).

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