Posted by
Northan, Brian on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Deconvolution-of-3D-SIM-data-tp6251420p6255092.html
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Commercial response from Media Cybernetics:
One thing to note is that depending on the sampling rate you may not get dots back even after deconvolution.
When interpreting OMX deconvolution results it may be useful to consider the differences between deconvolving widefield and confocal images.
In widefield the dominant effect of deconvolution is deblurring, thus the dramatic haze reduction. In confocal/two-photon/ the effect is a little different. The hardware has all ready done some deblurring at the expense of noise. So in these modalities the effect of deconvolution is some deblurring combined with noise reduction.
I have deconvolved some SI images from Optigrid and the Quorum Angstrom using Autoquant blind deconvolution. As when deconvolving confocal the result was some deblurring and some noise reduction resulting in an increased signal to noise.
So the expectation when deconvolving OMX is not necessarily that you get exactly a "dot" back (especially if the image is over-sampled) but to get increased contrast and less noise.
As the other posters have mentioned the situation is complicated by possible non-linear processing steps in SIM. And care must be taken when using deconvolution on a modality it is not optimized for.
We encourage anyone who is interested in deconvolving SIM images to give us feedback.
Thanks
Brian
-----Original Message-----
From: Confocal Microscopy List [mailto:
[hidden email]] On Behalf Of Andreas Bruckbauer
Sent: Friday, April 08, 2011 11:49 AM
To:
[hidden email]
Subject: Re: Deconvolution of 3D SIM data
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When i generate a PSF for deconvolution using suitable beads, then image the same beads again and deconvolve the image, i would expect to get really tiny dots. See e.g.
http://www.svi.nl/BeadsDeconvolutionExample
I would expect something similar for the OMX when the reconstruction is perfect and includes proper deconvolution. However we get larger features, still within the expected OMX resolution 120 nm in width and 300 nm in z, but no dots. I think there is still some improvement possible either in the setup of the instrument or the software.
best wishes
Andreas
-----Original Message-----
From: Hans <
[hidden email]>
To:
[hidden email]
Sent: Fri, 8 Apr 2011 10:46
Subject: Re: Deconvolution of 3D SIM data
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(*commercial response*)
Dear All,
As the previous responses by David and Dan already state very well, caution should be taken in straightforward applying deconvolution on top of reconstructed images from SIM systems since these might be the result of various non-linear processing steps.
Still, since it seems that there is room for improvement in at least some SIM reconstructions, and the current discussion also points in that direction, here at SVI we wonder about the need for a SIM deconvolution module. This would work directly on raw SIM data.
We would very much appreciate to get some off-listfeedback from (potential) SIM users for such a module.
Cheers, Hans
-- -------------------------------------------------------------------
dr. Hans T.M. van der Voort (
[hidden email])
Scientific Volume Imaging b.v., URL:
http://www.svi.nl/
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