Structured illumination microscopy with noise-controlled image reconstructions

Smith, C. S.; Slotman, J.; Schermelleh, L.; Chakrova, N.; Hari, S.; Vos, Y.; Hagen, C. W.; Mueller, M.; van Cappellen, W.; Houtsmuller, A.; Hoogenboom, J. P.; Stallinga, S.

doi:10.1101/2021.03.11.434940

bioRxiv · 10.1101/2021.03.11.434940

Structured illumination microscopy with noise-controlled image reconstructions

Smith, C. S.·Slotman, J.·Schermelleh, L.·Chakrova, N.·Hari, S.·Vos, Y.·Hagen, C. W.·Mueller, M.·van Cappellen, W.·Houtsmuller, A.·Hoogenboom, J. P.·Stallinga, S.

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Abstract

Super-resolution structured illumination microscopy (SIM) has become a widely used method for biological imaging. Standard reconstruction algorithms, however, are prone to generate noise-specific artefacts that limit their applicability for lower signal-to-noise data. Here, we present a physically realistic noise model that explains the structured noise artefact and that is used to motivate new complementary reconstruction approaches. True Wiener-filtered SIM optimizes contrast given the available signal-to-noise ratio, flat-noise SIM fully overcomes the structured noise artefact while maintaining resolving power. Both methods eliminate ad-hoc user adjustable reconstruction parameters in favour of physical parameters, enhancing objectivity. The new reconstructions point to a trade-off between contrast and a natural noise appearance. This trade-off can be partly overcome by additional notch filtering, but at the expense of a decrease in signal-to-noise ratio. The benefits of the proposed approaches are demonstrated on focal adhesion and tubulin samples in 2D and 3D, and on nano-fabricated fluorescent test patterns.

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Smith, C. S., Slotman, J., Schermelleh, L., Chakrova, N., Hari, S., Vos, Y., Hagen, C. W., Mueller, M., van Cappellen, W., Houtsmuller, A., Hoogenboom, J. P., Stallinga, S.. 2021-03-11. Structured illumination microscopy with noise-controlled image reconstructions. https://doi.org/10.1101/2021.03.11.434940

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