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Dear All,

sorry for the typo:
It's great to see that the topic is of interest to the Community, of course!
:0)

Have a nice weekend,
Dmitry
MIAWiki for Mass Collaboration:
Not Published = Lost Forever

On 26/11/2011 8:14 a.m., Dmitry Sokolov wrote:
> Hi Dan,
>
> thanks a lot. The procedure looks very good for trial. I regret now that information on the elastic alignment was added to MIAWiki a couple of months after it's actual need and is still of interest to the Community.
> I hope finding the topic will be quicker from now on through the MIAWiki interactive search bar and via the permalink to the page:
> http://confocal-manawatu.pbworks.com/w/page/40316645/Elastic%20Alignment%20of%20Images%20ImageJ
> The page is cross-linked with "Manual Stack Alignment"
> http://confocal-manawatu.pbworks.com/w/page/38604941/Manual%20Stack%20Alignment#view=page
> and a couple of other knowledge nodes in accordance to principles of Contextual Integration:
> http://confocal-manawatu.pbworks.com/w/page/47947288/Contextual%20Integration
>
> Thanks again,
> Dmitry
> MIAWiki for Mass Collaboration:
> Not Published = Lost Forever
>
> On 25/11/2011 10:04 p.m., Daniel James White wrote:
>> 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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