Re: How does Multiview-Reconstruction compare to Zeiss?

Posted by Mario Emmenlauer-3 on Nov 05, 2014; 12:11pm
URL: http://imagej.273.s1.nabble.com/How-does-Multiview-Reconstruction-compare-to-Zeiss-tp5010290p5010310.html

Dear Pavel,

thanks a lot for the detailed and helpful answer! Below more:

On 05.11.2014 11:07, Pavel Tomancak wrote:

>> I'm trying to automate the workflow from a Zeiss Lightsheet Z.1 to
>> the registered/fused/deconvolved volume. Previously we used the Zeiss
>> software, but I understand that this can not easily be scripted and/or
>> distributed on a cluster?
>>
>> What is the best replacement that is scriptable and cluster-runnable?
>
> In addition to what you already found, there is also this web page
>
> http://fiji.sc/SPIM_Registration_on_cluster
>
> which details how to run Fiji's SPIMage processing pipelines on a cluster (registration, fusion, deconvolution and HDF5 saving).

I will check this out, thanks!

>> I've found http://fiji.sc/Multiview-Reconstruction (MR) and it looks
>> very promising, but how does it exactly compare to the Zeiss software?
>
> We worked very closely with Zeiss when developing the Fiji plugins. The Zeiss software is to a large degree based on our published research:
>
> Preibisch S., Saalfeld S., Schindelin J., Tomancak P. (2010) Software for bead-based registration of selective plane illumination microscopy data. Nature Methods 7:418-419
>
> In ZEN it has been implemented by Zeiss developers independently and since it is not published and the source code is not available I cannot say how similar it is to our implementation when it comes to details. The general approach is similar. As far as I know, Zeiss software does not use global optimisation.
>
>> I understand Zeiss does not require beads, MR does?
>
> Zeiss software can do the reconstruction with and without beads. Similarly the Fiji plugins can either use beads or segmentation in the sample (e.g. nuclei) to achieve the registration. Sometimes it is necessary to use both, first bead-based followed by nuclei based registration. For example look here
>
> http://openspim.org/TriboliumExtraembryonicMembranes

Thanks, this is very enlightening and helpful. I will check
this in more detail and see how we can profit from segmentation
versus beads...


>> 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?

>> 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. 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/

Is there any other (commercial or non-commercial) option you would be
aware of?

All the best and thanks a lot,

    Mario



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