software stitchs multiple z-stack along z

[dbstongy]

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Dear All,

May I have your suggestion that which software can be used to combine stacks of images (plane or 3D) to make a single 3D version? For instance, I want to use ten 1mm-thick tissue sections to generate a 10mm-thick 3D image.

Appreciate any feedback.

Thank you.
TONG Yan
NUS Centre for BioImaging Sciences
Department of Biological Sciences
National University of Singapore

[Daniel James White]

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Hi TONG Yan

there are open source tools in the Fiji disrtibution of imageJ
that can likely do this job.
Read the docs
search for stitching

http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)

Dan



On Nov 15, 2011, at 7:04 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Tue, 15 Nov 2011 08:56:42 +0800
> From:    Tong Yan <[hidden email]>
> Subject: software stitchs multiple z-stack along z
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> Dear All,
>
> May I have your suggestion that which software can be used to combine stack=
> s of images (plane or 3D) to make a single 3D version? For instance, I want=
> to use ten 1mm-thick tissue sections to generate a 10mm-thick 3D image.
>
> Appreciate any feedback.
>
> Thank you.
> TONG Yan
> NUS Centre for BioImaging Sciences
> Department of Biological Sciences
> National University of Singapore

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 )

[Janne Hyötylä]

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Hi,

Check out XuvTools:
http://www.xuvtools.org/

I haven't used it myself but heard people recommend it on several  
occasions.

Cheers
Janne


On Tue, 15 Nov 2011 01:56:42 +0100, Tong Yan <[hidden email]> wrote:

> Dear All,
>
> May I have your suggestion that which software can be used to combine  
> stacks of images (plane or 3D) to make a single 3D version? For  
> instance, I want to use ten 1mm-thick tissue sections to generate a  
> 10mm-thick 3D image.
>
> Appreciate any feedback.
>
> Thank you.
> TONG Yan
> NUS Centre for BioImaging Sciences
> Department of Biological Sciences
> National University of Singapore

[Bjornsson, Chris]

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Hello,

You can also check out FARSIGHT, which is capable of joint registering large datasets while tolerating variable overlap, rotations and shifts in Z. Check out Tsai et al. (2011) J. Microsc. 243(2):154-71.

Cheers,
Chris

Chris Bjornsson
Director, Microscopy Core
Director, Cell & Molecular Core
Director, Stem Cell Core
Research Assistant Professor, Department of Biology
Center for Biotechnology & Interdisciplinary Studies, Room 2149
Rensselaer Polytechnic Institute
110 8th St., Troy, NY 12180
ph. 518-276-3456

________________________________________
From: Confocal Microscopy List [[hidden email]] on behalf of Janne Hyötylä [[hidden email]]
Sent: Tuesday, November 15, 2011 4:43 AM
To: [hidden email]
Subject: Re: software stitchs multiple z-stack along z

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Hi,

Check out XuvTools:
http://www.xuvtools.org/

I haven't used it myself but heard people recommend it on several
occasions.

Cheers
Janne


On Tue, 15 Nov 2011 01:56:42 +0100, Tong Yan <[hidden email]> wrote:

> Dear All,
>
> May I have your suggestion that which software can be used to combine
> stacks of images (plane or 3D) to make a single 3D version? For
> instance, I want to use ten 1mm-thick tissue sections to generate a
> 10mm-thick 3D image.
>
> Appreciate any feedback.
>
> Thank you.
> TONG Yan
> NUS Centre for BioImaging Sciences
> Department of Biological Sciences
> National University of Singapore

[Mario Emmenlauer]

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Hi,

xuvtools is great for many kinds of stitchings, but only works if there is
some overlap between the stacks. So for a stitching of 2D-planes-along-Z,
it won't work. Sorry to say that :-(

All the best,

    Mario

> Hi,
>
> Check out XuvTools:
> http://www.xuvtools.org/
>
> I haven't used it myself but heard people recommend it on several
> occasions.
>
> Cheers
> Janne
>
>
> On Tue, 15 Nov 2011 01:56:42 +0100, Tong Yan <[hidden email]> wrote:
>
>> Dear All,
>>
>> May I have your suggestion that which software can be used to combine
>> stacks of images (plane or 3D) to make a single 3D version? For
>> instance, I want to use ten 1mm-thick tissue sections to generate a
>> 10mm-thick 3D image.
>>
>> Appreciate any feedback.
>>
>> Thank you.
>> TONG Yan
>> NUS Centre for BioImaging Sciences
>> Department of Biological Sciences
>> National University of Singapore
>
>

[Bjornsson, Chris]

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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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Hi Tong Yan,

Depending on the method of tissue preparation (viz. sectioning), FARSIGHT can pull this off. Vibratome sectioning tends to erode some tissue as it saws through the block, frustrating efforts to stitch together adjacent slices (we've tried). Feel free to contact me offline if you'd like to pursue/discuss this further...

Cheers,
Chris

Chris Bjornsson
Director, Microscopy Core
Director, Cell & Molecular Core
Director, Stem Cell Core
Research Assistant Professor, Department of Biology
Center for Biotechnology & Interdisciplinary Studies, Room 2149
Rensselaer Polytechnic Institute
110 8th St., Troy, NY 12180
ph. 518-276-3456

________________________________________
From: Confocal Microscopy List [[hidden email]] on behalf of Mario Emmenlauer [[hidden email]]
Sent: Wednesday, November 16, 2011 3:35 AM
To: [hidden email]
Subject: Re: software stitchs multiple z-stack along z

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Hi,

xuvtools is great for many kinds of stitchings, but only works if there is
some overlap between the stacks. So for a stitching of 2D-planes-along-Z,
it won't work. Sorry to say that :-(

All the best,

    Mario

> Hi,
>
> Check out XuvTools:
> http://www.xuvtools.org/
>
> I haven't used it myself but heard people recommend it on several
> occasions.
>
> Cheers
> Janne
>
>
> On Tue, 15 Nov 2011 01:56:42 +0100, Tong Yan <[hidden email]> wrote:
>
>> Dear All,
>>
>> May I have your suggestion that which software can be used to combine
>> stacks of images (plane or 3D) to make a single 3D version? For
>> instance, I want to use ten 1mm-thick tissue sections to generate a
>> 10mm-thick 3D image.
>>
>> Appreciate any feedback.
>>
>> Thank you.
>> TONG Yan
>> NUS Centre for BioImaging Sciences
>> Department of Biological Sciences
>> National University of Singapore
>
>

[Deanne Veronica Catmull]

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I think the new Zeiss Zen software allows you to tile in Z allowing you to stitch various stacks over large areas. Only useful though if you have a Zeiss scope.

Kind regards,
Deanne.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Tong Yan
Sent: Tuesday, 15 November 2011 11:57 AM
To: [hidden email]
Subject: software stitchs multiple z-stack along z

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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Dear All,

May I have your suggestion that which software can be used to combine stacks of images (plane or 3D) to make a single 3D version? For instance, I want to use ten 1mm-thick tissue sections to generate a 10mm-thick 3D image.

Appreciate any feedback.

Thank you.
TONG Yan
NUS Centre for BioImaging Sciences
Department of Biological Sciences
National University of Singapore

[B. Prabhakar Pandian]

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Hello,
              I am emailing to see if anybody has a suggestion for a
cell viability/toxicity assay that works similar to LDH/Caspase but
relies on internal enzymes rather than in the supernatant.  In addition,
it should be compatible with fluorescence microscope.

Thanks,

-Prabhakar

[Iain Johnson]

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Calcein AM  (intracellular esterase substrate).  Incubate cells for 10
minutes in 1 microM calcein AM in serum-free medium at 37C.  Wash off
staining medium and replace with complete culture medium.  Image in
FITC/GFP channel.

You can also add a second dimension to the assay (at the expense of giving
up more spectral real estate).

SYTOX Orange (Molecular Probes; membrane permeability probe).  Add to
complete culture medium at 5 microM.  Do not wash.  Image in TRITC/Cy3
channel.

Iain

Iain Johnson Consulting
Eugene, OR
[phone]

On Thu, Nov 17, 2011 at 7:23 AM, B. Prabhakar Pandian <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> *****
>
> Hello,
>             I am emailing to see if anybody has a suggestion for a cell
> viability/toxicity assay that works similar to LDH/Caspase but relies on
> internal enzymes rather than in the supernatant.  In addition, it should be
> compatible with fluorescence microscope.
>
> Thanks,
>
> -Prabhakar
>