Posted by
Pavel Tomancak on
Nov 05, 2014; 10:07am
URL: http://imagej.273.s1.nabble.com/How-does-Multiview-Reconstruction-compare-to-Zeiss-tp5010290p5010308.html
Dear Mario,
> 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_clusterwhich details how to run Fiji's SPIMage processing pipelines on a cluster (registration, fusion, deconvolution and HDF5 saving).
> 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> 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.
> 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/1308.0730http://fiji.sc/Multi-View_Deconvolutionvisualisation solution for multi-view SPIM data - BigDataViewer (to be published soon)
http://fiji.sc/BigDataViewerand 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_microscopyDon't hesitate to contact us if you have further questions.
All the best
PAvel
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