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Hi Emma, Hi Dimitry,
On Nov 25, 2011, at 7:02 AM, CONFOCALMICROSCOPY automatic digest system wrote:
> Date: Tue, 22 Nov 2011 07:57:48 +1300
> From: Dmitry Sokolov <[log in to unmask]>
> Subject: Re: 3D reconstruction of multiple, fluorescently labelled, sections
>
> Hi Emma,
>
> StackReg plugin did not work for me on a very similar task a couple of ye=
> ars ago. The slices were found not only rotated on the slides but also de=
> formed at cutting. Automatic alignment without absolute reference points =
> or sites can be problematic if not impossible due to the distortions espe=
> cially.
> My experience on the subject is summarized here:
> http://confocal-manawatu.pbworks.com/w/page/38604941/Manual%20Stack%20Ali=
> gnment
>
> I would appreciate to hear a better solution if available.
This problem has been solved for electron microscopy, and the solution is appicable to fluorescence microscopy.
The software solutions are available in Fiji already,
and are the work of the Tomancak lab here at MPI-CBG.
see info here:
http://fiji.sc/wiki/index.php/Elastic_Alignment_and_Montage
what you get is :
Elastic registration of the image slices,
so in the reconstruction objects dont joggle and jitter as you go through the z stack.
here we have multiple z stack that need to be aligned,
but the solutions in this software can be adapted to deal with that.
So long as there is overlapping information between the ends of the stacks, all is well.
cheers
Dan
>
> Please feel free to modify the MIAWiki and contact me offline when requir=
> ed.
>
> With best wishes,
> Dmitry
> MIAWiki for Mass Collaboration
Dr. Daniel James White BSc. (Hons.) PhD
Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany
+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)
chalkie666 Skype
http://www.bioimagexd.net BioImageXD
http://fiji.sc Fiji - is just ImageJ (Batteries Included)
http://www.chalkie.org.uk Dan's Homepages
https://ifn.mpi-cbg.de Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )
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