SPIM Fusion / Reconstruction

[Mario Emmenlauer]

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Dear All,

I'm trying to automate the workflow from a Zeiss Lightsheet Z.1 up
until the registered/fused/deconvolved volume. Ideally I would like to
achieve as high automation as possible, and produce the fused volume
as quickly as possible. For this purpose I'm trying to evaluate the
available options and compile a small review. So far, we use the Zeiss
Zen software, but now we are looking for alternatives that are more
easily portable to a cluster / grid environment, that are more robust,
and that allow for better automation. Upfront I don't have any fixed
constraints, so solutions may require beads, or specific hardware to
work. With the help of the ImageJ/Fiji mailing list I could find:

(1) Zeiss Zen software, closed source
(2) Spim Registration from Preibisch et al., built into Fiji, open
    source, with very good usage instructions here:
    Schmied C., Stamataki E., Tomancak P. (2014) Open-source solutions
    for SPIMage processing. Methods Cell Biol., 123, pp. 505-529
    Cluster usage: http://fiji.sc/SPIM_Registration_on_cluster
(3) Multiview-Reconstruction from Preibisch et al., successor of (2),
    built into Fiji via BigDataViewer, open source, with instructions:
    http://fiji.sc/Multiview-Reconstruction
(4) Lucy-Richardson Deconvolution for Fusion (without software), LMB
    Freiburg: http://lmb.informatik.uni-freiburg.de/Publications/2011/BRT11/

Are there other solutions for (parts of) the process of SPIM fusion?

Thanks for feedback, and all the best,

   Mario




--
Mario Emmenlauer BioDataAnalysis             Mobil: [phone]
Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
D-81669 München                          http://www.biodataanalysis.de/

[Feinstein, Timothy]

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Hi Mario,

We have had a positive experience with TeraStitcher, a free plugin
developed for Vaa3D by a team in Italy (BMC Bioinformatics 2012, 13:316).
It stitches volumes nicely, but I would recommend it even more for how
well the team optimized it to work fast on the medium-power machines that
ordinary mortals use.  I believe that it creates five levels of de-rezzing
and then stitches the lowest res version first, then the next and it only
takes on the terabyte volume after it has already gotten very close.  It
gives you the option of saving each level so you can have a 500KB file for
GIFs, a 10 MB file for presentations, all the way up to the 4+ TB
original.  On the downside it can only handle one color at a time and the
interface takes time to learn.  I have made a cheater sheet to explain its
syntax that I can send it to anyone who wants it.

Many labs that do cutting edge SPIM swear by the Arivis Vision commercial
software package.  I have no experience with Arivis and cannot even give a
ballpark guess of its cost, but it should definitely be on the list.

Does anyone know if Imaris, Volocity or SVI are working on modules for
this?  SPIM stitching seems like it should fit right in their wheelhouse.

All the best,


Tim

Timothy Feinstein, Ph.D. | Manager, Core for
Confocal Microscopy and Quantitative Imaging
333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
Phone: [phone] | Email: [hidden email]







On 11/13/14, 2:58 AM, "Mario Emmenlauer" <[hidden email]> wrote:

>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://scanmail.trustwave.com/?c=129&d=ifLk1Czr4_JtquljfcGWa3N4gNKcjCiwmNf
>Gn58NJw&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic
>roscopy
>Post images on
>http://scanmail.trustwave.com/?c=129&d=ifLk1Czr4_JtquljfcGWa3N4gNKcjCiwmIL
>HzZVZdw&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your
>posting.
>*****
>
>Dear All,
>
>I'm trying to automate the workflow from a Zeiss Lightsheet Z.1 up
>until the registered/fused/deconvolved volume. Ideally I would like to
>achieve as high automation as possible, and produce the fused volume
>as quickly as possible. For this purpose I'm trying to evaluate the
>available options and compile a small review. So far, we use the Zeiss
>Zen software, but now we are looking for alternatives that are more
>easily portable to a cluster / grid environment, that are more robust,
>and that allow for better automation. Upfront I don't have any fixed
>constraints, so solutions may require beads, or specific hardware to
>work. With the help of the ImageJ/Fiji mailing list I could find:
>
>(1) Zeiss Zen software, closed source
>(2) Spim Registration from Preibisch et al., built into Fiji, open
>    source, with very good usage instructions here:
>    Schmied C., Stamataki E., Tomancak P. (2014) Open-source solutions
>    for SPIMage processing. Methods Cell Biol., 123, pp. 505-529
>    Cluster usage:
>http://scanmail.trustwave.com/?c=129&d=ifLk1Czr4_JtquljfcGWa3N4gNKcjCiwmNG
>VnsJadw&u=http%3a%2f%2ffiji%2esc%2fSPIM%5fRegistration%5fon%5fcluster
>(3) Multiview-Reconstruction from Preibisch et al., successor of (2),
>    built into Fiji via BigDataViewer, open source, with instructions:
>    
>http://scanmail.trustwave.com/?c=129&d=ifLk1Czr4_JtquljfcGWa3N4gNKcjCiwmIT
>JnMJZdw&u=http%3a%2f%2ffiji%2esc%2fMultiview-Reconstruction
>(4) Lucy-Richardson Deconvolution for Fusion (without software), LMB
>    Freiburg:
>http://scanmail.trustwave.com/?c=129&d=ifLk1Czr4_JtquljfcGWa3N4gNKcjCiwmIT
>Bz5EOIg&u=http%3a%2f%2flmb%2einformatik%2euni-freiburg%2ede%2fPublications
>%2f2011%2fBRT11%2f
>
>Are there other solutions for (parts of) the process of SPIM fusion?
>
>Thanks for feedback, and all the best,
>
>   Mario
>
>
>
>
>--
>Mario Emmenlauer BioDataAnalysis             Mobil: [phone]
>Balanstrasse 43                    mailto: mario.emmenlauer *
>http://scanmail.trustwave.com/?c=129&d=ifLk1Czr4_JtquljfcGWa3N4gNKcjCiwmNj
>CzZMLJA&u=http%3a%2f%2funibas%2ech
>D-81669 München  
>http://scanmail.trustwave.com/?c=129&d=ifLk1Czr4_JtquljfcGWa3N4gNKcjCiwmIO
>TzcYLJQ&u=http%3a%2f%2fwww%2ebiodataanalysis%2ede%2f