3D reconstruction of multiple, fluorescently labelled, sections

[Emma King-2]

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We would like to take serial sections (20 microns thick) of rat spinal
cord (up to 1cm long), label them with a bright and specific fluorescent
label, acquire images (we can use either a widefield or confocal
microscope) and then reconstruct the data in to one, 3D structure.

We have the sectioning, staining and acquisition parameters/options
under control, but don't have any software capable of reconstructing
the resultant images. Does anyone have any suggestions as to what
software to use and where to get it from?

Any help much appreciated.

Cheers,
Emma

Advanced Microscopy Unit
School of Biomedical Sciences
Univeristy of Nottingham

[Louis Villeneuve]

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Hi Emma,

In fact you want to add mutltiple Z-series together in order to form one
huge serie.  First, you will need a good computer and 2nd, I have done it
using Huygens software (SVI).
Also, I am pretty sure that there is a plugin In" Image J" that can do
that.  Do not forget to do that with a good computer!!!!

Best regards,

Louis

Louis Villeneuve
Associé de recherche - Microscopie confocale
Institut de Cardiologie de Montreal- Centre de recherche
5000 est Bélanger
Montreal (Qc), Canada
H1T 3C8

514-376-3330 ext 3511
514-376-1355 (fax)



Emma King <[hidden email]>@LISTS.UMN.EDU
Envoyé par : Confocal Microscopy List <[hidden email]>
2011-11-18 09:39
Veuillez répondre à
Confocal Microscopy List <[hidden email]>


A
[hidden email]
cc

Objet
3D reconstruction of multiple, fluorescently labelled, sections








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We would like to take serial sections (20 microns thick) of rat spinal
cord (up to 1cm long), label them with a bright and specific fluorescent
label, acquire images (we can use either a widefield or confocal
microscope) and then reconstruct the data in to one, 3D structure.

We have the sectioning, staining and acquisition parameters/options
under control, but don't have any software capable of reconstructing
the resultant images. Does anyone have any suggestions as to what
software to use and where to get it from?

Any help much appreciated.

Cheers,
Emma

Advanced Microscopy Unit
School of Biomedical Sciences
Univeristy of Nottingham

[Louis Kerr]

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Hi Emma,

Have you seen the work from Stephen Smith's Lab at Stanford with array tomography? This is a link to a Cold Spring Harbor Protocol.

http :// cshprotocols . cshlp .org/content/2010/11/ pdb .top89.full

Good luck,
Louie

----- Original Message -----
From: "Emma King" < emma .[hidden email]>
To: CONFOCALMICROSCOPY @LISTS. UMN . EDU
Sent: Friday, November 18, 2011 9:39:57 AM
Subject: 3D reconstruction of multiple, fluorescently labelled , sections

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We would like to take serial sections (20 microns thick) of rat spinal
cord (up to 1cm long), label them with a bright and specific fluorescent
label, acquire images (we can use either a widefield or confocal
microscope) and then reconstruct the data in to one, 3D structure.

We have the sectioning, staining and acquisition parameters/options
under control, but don't have any software capable of reconstructing
the resultant images. Does anyone have any suggestions as to what
software to use and where to get it from?

Any help much appreciated.

Cheers,
Emma

Advanced Microscopy Unit
School of Biomedical Sciences
Univeristy of Nottingham


--



Louis Kerr
lkerr @ mbl . edu

Research and Education Support Coordinator
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA 02543
508-289-7273
508-540-6902 (FAX)
508-292-0289 (Cell phone)

VISIT OUR WEB SITES:
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www .courses. mbl . edu

[tineke vendrig]

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We use the Andor software for our 3D movies, works nice and good!

Tineke Vendrig

--
Tineke Vendrig, ing
technical engineer optical microscopy
Delft University of Technology
Bionano Science
Kavli Institute of Nanoscience
Lorentzweg 1
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room F185
Tel: [phone]
Fax:[phone]
email: [hidden email]
mobile phone: [phone]


2011/11/18 Emma King <[hidden email]>

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We would like to take serial sections (20 microns thick) of rat spinal
> cord (up to 1cm long), label them with a bright and specific fluorescent
> label, acquire images (we can use either a widefield or confocal
> microscope) and then reconstruct the data in to one, 3D structure.
>
> We have the sectioning, staining and acquisition parameters/options
> under control, but don't have any software capable of reconstructing
> the resultant images. Does anyone have any suggestions as to what
> software to use and where to get it from?
>
> Any help much appreciated.
>
> Cheers,
> Emma
>
> Advanced Microscopy Unit
> School of Biomedical Sciences
> Univeristy of Nottingham
>

[Johannes Schindelin]

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On Fri, 18 Nov 2011, [hidden email] wrote:

> Emma King <[hidden email]>@LISTS.UMN.EDU
> Envoyé par : Confocal Microscopy List <[hidden email]>
> 2011-11-18 09:39
>
> > We would like to take serial sections (20 microns thick) of rat spinal
> > cord (up to 1cm long), label them with a bright and specific
> > fluorescent label, acquire images (we can use either a widefield or
> > confocal microscope) and then reconstruct the data in to one, 3D
> > structure.
>
> > We have the sectioning, staining and acquisition parameters/options
> > under control, but don't have any software capable of reconstructing
> > the resultant images. Does anyone have any suggestions as to what
> > software to use and where to get it from?
>
> In fact you want to add mutltiple Z-series together in order to form one
> huge serie.  First, you will need a good computer and 2nd, I have done
> it using Huygens software (SVI).
>
> Also, I am pretty sure that there is a plugin In" Image J" that can do
> that.  Do not forget to do that with a good computer!!!!

If all you want to do is a volume rendering, there are indeed 2 ImageJ
plugins to do the job: Volume Viewer (non-accelerated) and 3D Viewer (this
one uses your graphics adapter's accelerated 3D rendering).

However, if you need to have surface models, you might want to look into
the TrakEM2 plugin. It is very powerful, therefore it takes some training
before one can exploit its capabilities in full.

If you do not want to bother to find all the bits and pieces required for
these plugins to run, please feel free to download Fiji (http://fiji.sc/)
which bundles ImageJ with a lot of plugins (including the 3 mentioned
above).

Ciao,
Johannes

[Armstrong, Brian]

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You could try Reconstruct from NIH Human Brain project (http://synapses.clm.utexas.edu/tools/reconstruct/reconstruct.stm ).

In my opinion, Amira, Imaris, and Volocity, are probably best at 3D visualization tools.

Cheers,

Brian D Armstrong PhD
Assistant Research Professor
Light Microscopy Core
Beckman Research Institute
City of Hope
Dept of Neuroscience
1450 E Duarte Rd
Duarte, CA 91010
626-256-4673 x62872

http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imaging/Pages/default.aspx


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Johannes Schindelin
Sent: Friday, November 18, 2011 10:19 AM
To: [hidden email]
Subject: Re: RE 3D reconstruction of multiple, fluorescently labelled, sections

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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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On Fri, 18 Nov 2011, [hidden email] wrote:

> Emma King <[hidden email]>@LISTS.UMN.EDU
> Envoyé par : Confocal Microscopy List <[hidden email]>
> 2011-11-18 09:39
>
> > We would like to take serial sections (20 microns thick) of rat spinal
> > cord (up to 1cm long), label them with a bright and specific
> > fluorescent label, acquire images (we can use either a widefield or
> > confocal microscope) and then reconstruct the data in to one, 3D
> > structure.
>
> > We have the sectioning, staining and acquisition parameters/options
> > under control, but don't have any software capable of reconstructing
> > the resultant images. Does anyone have any suggestions as to what
> > software to use and where to get it from?
>
> In fact you want to add mutltiple Z-series together in order to form one
> huge serie.  First, you will need a good computer and 2nd, I have done
> it using Huygens software (SVI).
>
> Also, I am pretty sure that there is a plugin In" Image J" that can do
> that.  Do not forget to do that with a good computer!!!!

If all you want to do is a volume rendering, there are indeed 2 ImageJ
plugins to do the job: Volume Viewer (non-accelerated) and 3D Viewer (this
one uses your graphics adapter's accelerated 3D rendering).

However, if you need to have surface models, you might want to look into
the TrakEM2 plugin. It is very powerful, therefore it takes some training
before one can exploit its capabilities in full.

If you do not want to bother to find all the bits and pieces required for
these plugins to run, please feel free to download Fiji (http://fiji.sc/)
which bundles ImageJ with a lot of plugins (including the 3 mentioned
above).

Ciao,
Johannes


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[Graham Wright]

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Hi Emma,

Sorry for contributing a bit late to this discussion or if somebody has
already mentioned this (I didn't see it if so).

If you make the 'huge series' using ImageJ/Fiji (in Fiji through
Image>Stacks>Manipulation) you can then try to use the StackReg plugin from
EPFL (http://bigwww.epfl.ch/thevenaz/stackreg/) which requires the turboreg
plugin, linked from the same site, to align the stack (these are both built
into Fiji in Plugins>Registration). Follow this with some cropping and it
might work out for further use in any of the 3D visualisation programs
discussed.

If each image shares enough overlap/similarity with the previous it should
work.

Good luck,
Graham

--
IMB Microscopy Unit
Institute of Medical Biology
Singapore
http://www.imb.a-star.edu.sg/imu/index.html

On 18 November 2011 22:39, Emma King <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We would like to take serial sections (20 microns thick) of rat spinal
> cord (up to 1cm long), label them with a bright and specific fluorescent
> label, acquire images (we can use either a widefield or confocal
> microscope) and then reconstruct the data in to one, 3D structure.
>
> We have the sectioning, staining and acquisition parameters/options
> under control, but don't have any software capable of reconstructing
> the resultant images. Does anyone have any suggestions as to what
> software to use and where to get it from?
>
> Any help much appreciated.
>
> Cheers,
> Emma
>
> Advanced Microscopy Unit
> School of Biomedical Sciences
> Univeristy of Nottingham
>

[phil laissue]

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Hi Emma

I am very happy with Nikon's NIS-Elements software, but just wanted to
second Graham Wright's & Louis Kerr's input - the stackreg algorithm works
a charm. I often use its modified version MultiStackReg, aligning one
channel and applying the same translation to the other(s). Very useful in
case of moving cells, stage drift etc.

http://www.stanford.edu/~bbusse/work/downloads.html

Speaking of which: Many thanks to Thierry Thévenaz & Michael Unser and Brad
Busse & Steven Smith for these fabulous open-source tools!

Philippe


Philippe Laissue, PhD
Bioimaging Facility, University of Essex, UK

[Dmitry Sokolov]

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Hi Emma,

StackReg plugin did not work for me on a very similar task a couple of years ago. The slices were found not only rotated on the slides but also deformed at cutting. Automatic alignment without absolute reference points or sites can be problematic if not impossible due to the distortions especially.
My experience on the subject is summarized here:
http://confocal-manawatu.pbworks.com/w/page/38604941/Manual%20Stack%20Alignment

I would appreciate to hear a better solution if available.

Please feel free to modify the MIAWiki and contact me offline when required.

With best wishes,
Dmitry
MIAWiki for Mass Collaboration
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Dr. Dmitry Sokolov
*LYNX Analytics: * Image Analysis - Data Processing - Knowledge Transfer
/Scanning Confocal / Atomic Force Microscopy & Spectroscopy/
Mob: [phone]

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


On 21/11/2011 10:58 p.m., Graham Wright wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Emma,
>
> Sorry for contributing a bit late to this discussion or if somebody has
> already mentioned this (I didn't see it if so).
>
> If you make the 'huge series' using ImageJ/Fiji (in Fiji through
> Image>Stacks>Manipulation) you can then try to use the StackReg plugin from
> EPFL (http://bigwww.epfl.ch/thevenaz/stackreg/) which requires the turboreg
> plugin, linked from the same site, to align the stack (these are both built
> into Fiji in Plugins>Registration). Follow this with some cropping and it
> might work out for further use in any of the 3D visualisation programs
> discussed.
>
> If each image shares enough overlap/similarity with the previous it should
> work.
>
> Good luck,
> Graham
>
> --
> IMB Microscopy Unit
> Institute of Medical Biology
> Singapore
> http://www.imb.a-star.edu.sg/imu/index.html
>
> On 18 November 2011 22:39, Emma King<[hidden email]>  wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****

>>
>> We would like to take serial sections (20 microns thick) of rat spinal
>> cord (up to 1cm long), label them with a bright and specific fluorescent
>> label, acquire images (we can use either a widefield or confocal
>> microscope) and then reconstruct the data in to one, 3D structure.
>>
>> We have the sectioning, staining and acquisition parameters/options
>> under control, but don't have any software capable of reconstructing
>> the resultant images. Does anyone have any suggestions as to what
>> software to use and where to get it from?
>>
>> Any help much appreciated.
>>
>> Cheers,
>> Emma
>>
>> Advanced Microscopy Unit
>> School of Biomedical Sciences
>> Univeristy of Nottingham
>>

[Daniel James White]

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Hi Emma,

> Date:    Mon, 21 Nov 2011 09:18:27 +0000
> From:    Emma King <[hidden email]>
> Subject: Re: CONFOCALMICROSCOPY Digest - 17 Nov 2011 to 18 Nov 2011 (#2011-88)

> Hi All,
>
> Thanks for all your messages. Louis described much better than I did what w=
> e plan to do "In fact you want to add multiple Z-series together in order t=
> o form one huge series"!

OK, then we also have tools for that kind of thing in Fiji.

>
> We have Volocity (and obviously imageJ) to visualise 3D data and I believe=
> we can add z-series together, on top of each other. My worry is we will ha=
> ve issues aligning structures in one z-stack, from one tissue section, with=
> the same structures in the next z-stack/tissue section.

Your worries are well founded, and possibly already solved.
See
http://fiji.sc/TrakEM2_align_sections_tutorial
http://bigwww.epfl.ch/thevenaz/stackreg/

and other tools in Fiji.

There is nothing that will just work out of the box,
but rather it wil take some figuring out, and possibly the
writing of at least a macro to automate the many mouse clicks.

If there is overlapping information in the top optical section of one stack
and the bottom ptical section of the next z stack from the next physical section,
then it might be possible to get the 3D stitching plugin to glue the z stacks together correctly.

http://fiji.sc/Stitching_2D/3D

http://fiji.sc/wiki/index.php/Stitching_2D/3D#2D_Stitching_and_3D_Stitching

(might need to "rotate" the z stacks first so that the z becomes x
for this plugin to work... or maybe not)

cheers

Dan





>
> I'll give it a go using the suggestions made and come back to you if I get =
> stuck!
>
> Thanks again,
> Em

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

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (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 )

[Kenton]

Hi
Just something to add: Personally I use Fiji for this and registration> 'register virtual stack slices' is better that stackreg for large stacks and can align one colour by another etc. But I was going to say that with multiple sections like yours if you are not after quantitative flourescence then it is really good to float the image around a mean and have a common standard deviation of intensities. If you want to do this you can write a macro (or ask me) in FIJI or use IMOD software (which is definitely better on files too large to hold in the ram).

If you are having trouble aligning but want a quantitative result then float the images align them but use the output alignment files to then align the original.
Regards
Kenton

[phil laissue]

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Tissue deformations due to cutting are tricky, and usually require pretty
heavy affine transformation (unless you photograph the block face, which
can't be used in this case). Derek Magee presented an elegant solution a
few years ago:
Magee D., Treanor D., and Quirke P., A New Image Registration algorithm
with application to 3D Histopathology *Proc. Microscopic Image Analysis
with Applications in Biology (MICCAI Workshop)*, 2008
I'm not sure about the availability of the algorithm, but you could contact
him directly via
http://www.comp.leeds.ac.uk/drm/
(where you'll also find the pdf of said paper).
There's many other approaches (e.g. Eric Bardinet et al.'s block matching
or Amelia Cifor/Tony Pridmore/Alain Pitiot's work), but again, I don't know
about algorithm availability - certainly no ImageJ plugins.

[Daniel James White]

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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 <[hidden email]>
> 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

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (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 )

[Dmitry Sokolov]

*****
To join, leave or search the confocal microscopy listserv, go to:
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*****

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<[hidden email]>
>> 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
>
> [phone] (German Mobile)
> [phone] (Work phone at MPI-CBG)
> [phone] (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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[Dmitry Sokolov]

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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<[hidden email]>
>>> 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
>>
>> [phone] (German Mobile)
>> [phone] (Work phone at MPI-CBG)
>> [phone] (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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