PT  - JOURNAL ARTICLE
AU  - Jakub Pospíšil
AU  - Tomáš Lukeš
AU  - Justin Bendesky
AU  - Karel Fliegel
AU  - Kathrin Spendier
AU  - Guy M. Hagen
TI  - Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction
AID  - 10.1101/426296
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 426296
4099  - http://biorxiv.org/content/early/2018/09/25/426296.short
4100  - http://biorxiv.org/content/early/2018/09/25/426296.full
AB  - Background Structured illumination microscopy (SIM) is a family of methods in optical fluorescence microscopy that can achieve both optical sectioning and super-resolution effects. SIM is a valuable method for high resolution imaging of fixed cells or tissues labeled with conventional fluorophores, as well as for imaging the dynamics of live cells expressing fluorescent protein constructs. In SIM, one acquires a set of images with shifting illumination patterns. This set of images is subsequently treated with image analysis algorithms to produce an image with reduced out-of-focus light (optical sectioning) and/or with improved resolution (super-resolution).Findings Five complete and freely available SIM datasets are presented including raw and analyzed data. We report methods for image acquisition and analysis using open source software along with examples of the resulting images when processed with different methods. We processed the data using established optical sectioning SIM and super-resolution SIM methods, and with newer Bayesian restoration approaches which we are developing.Conclusion Various methods for SIM data acquisition and processing are actively being developed, but complete raw data from SIM experiments is not typically published. Publicly available, high quality raw data with examples of processed results will aid researchers when developing new methods in SIM. Biologists will also find interest in the high-resolution images of animal tissues and cells we acquired. All of the data was processed with SIMToolbox, an open source and freely available software solution for SIM.GFPgreen fluorescent proteinNAnumerical aperturePSFpoint spread functionWFwide fieldSIMstructured illumination microscopyPSDpower spectral densityPSDcacircularly averaged power spectral densitySNRsignal to noise ratioSBRsignal to background ratio