Posted by
Pavel Tomancak on
Nov 05, 2014; 12:36pm
URL: http://imagej.273.s1.nabble.com/How-does-Multiview-Reconstruction-compare-to-Zeiss-tp5010290p5010311.html
>>> And our workflow
>>> uses DualSide Fusion, is that supported with MR?
>>
>> The DualSide Fusion in done internally in ZEN. We simply start our pipelines with the fused data (i.e. left and right lightsheet merged). It is important to save the data from ZEN as one file per view per time point. This is currently the only dataset that Fiji Bioformat importer can reliably open. Efforts to make it more robust are underway.
>
> My biologists report that the DualSide Fusion with the Zeiss Zen
> Software is sometimes done while recording, but this only works for
> small Z-stacks for them, because for big stacks it takes the computer
> too long and imaging gets delayed. So I understand that this is a
> bottleneck for us - did you get this solved somehow?
I don't think we have seen this problem. I cc Christopher Schmied who has more hands on experience.
>
>
>>> Finally, how do they
>>> compare in terms of quality of the result, is one or the other software
>>> "better" in any aspect by a reasonable margin, or do they compare on
>>> par?
>>
>> Ok, this is very hard to answer. We are academic researchers and of course we believe that our approach is the best ;-). We have not done rigorous benchmarks against Zeiss software. Anecdotally, on some datasets Fiji works better on others ZEN. You will have to try it for yourself.
>>
>> Here are some additional resources that you may find useful.
>>
>> A book chapter describing the SPIMage processing pipeline formally, tutorial style (download it from here
http://www.mpi-cbg.de/nc/research/research-groups/pavel-tomancak/papers.html)
>> Schmied C., Stamataki E., Tomancak P. (2014) Open-source solutions for SPIMage processing. Methods Cell Biol., 123, pp. 505-529
>>
>> Multi-view deconvolution paper and software (this is, I think, unrelated to the Zeiss deconvolution approach - an alternative).
>> Preibisch S., Amat F., Stamataki E., Sarov M., Myers E., Tomancak P. (2013) Efficient bayesian multi-view deconvolution Nature Methods, 7, 418–419
http://arxiv.org/abs/1308.0730>>
>>
http://fiji.sc/Multi-View_Deconvolution>>
>> visualisation solution for multi-view SPIM data - BigDataViewer (to be published soon)
>>
http://fiji.sc/BigDataViewer>>
>> and finally lots of useful information can be found on the OpenSPIM wiki, particularly in the section dealing with the EMBO course on light sheet microscopy that we organised in Dresden this summer
>>
>>
http://openspim.org/EMBO_practical_course_Light_sheet_microscopy>>
>> Don't hesitate to contact us if you have further questions.
>
> I've read already a bit on OpenSPIM, it looks very interesting! Do
> I understand correctly that OpenSPIM does not develop or host software
> for registration/fusion/deconvolution itself, the software recommended
> at OpenSPIM is basically the same Fiji modules you mention also above?
> It makes perfect sense, but I'm trying to make sure I'm not overlooking
> any (reasonably good) software.
Exactly, the SPIMage processing software in Fiji applies both to data from LZ1 and OpenSPIM. There is no principal difference, just different data format wrangling issues.
> The only other software for fusion I
> could find is "Spatially-Variant Lucy-Richardson Deconvolution for
> Multiview Fusion of Microscopical 3D Images" by Maja Temerinac-Ott et
> al, see
http://lmb.informatik.uni-freiburg.de/Publications/2011/BRT11/The problem is that as far as I know this is not a software but a paper. It is very unlikely that this approach would scale to large images. But feel free to contact Maja, I am sure she has some code.
>
> Is there any other (commercial or non-commercial) option you would be
> aware of?
I don't know of any solution that would be usable as a downloadable software. There are several papers, like for example
http://www.ncbi.nlm.nih.gov/pubmed/22072386http://www.ncbi.nlm.nih.gov/pubmed/17339847 (this deconvolution methods has been reimplemented by Stephan Preibisch in Java as part of the deconvolution paper I mentioned before, I don't know if he released that code, he is currently on vacation)
http://www.ncbi.nlm.nih.gov/pubmed/19547131All the best
PAvel
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