Serial block face sectioning with confocal/multiphoton imaging

classic Classic list List threaded Threaded
10 messages Options
Kathryn Spencer Kathryn Spencer
Reply | Threaded
Open this post in threaded view
|

Serial block face sectioning with confocal/multiphoton imaging

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi all;
                Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
                Thanks so much.
                Kathy Spencer


The Scripps Research Institute
Dept of Molecular and Cellular Neuroscience
10550 N. Torrey Pines Road
DNC 216
La Jolla, Ca 92037
Andrea Stout Andrea Stout
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Kathy,

Some researchers from my institution recently applied for funds to purchase the TissueCyte 1000 system from TissueVision:

http://www.tissuevision.com/ <http://www.tissuevision.com/>

It uses multi-photon imaging with serial sectioning and 3D image reconstruction to image whole organs. I have never seen it demo’ed and have no commercial interest, but it sounds like something you might be interested in.  Best,

Andrea

Andrea L. Stout, Ph. D.
Director,  CDB Microscopy Core Facility
Perelman School of Medicine at the University of Pennsylvania
1107 BRB 2/3
421 Curie Boulevard
Philadelphia, PA 19104

phone: 215-573-3942
email: [hidden email]
web: http://www.med.upenn.edu/cdbmicroscopycore/

Twitter: @CDBMicroCore
Instagram: @cdbmicrocore







> On Jun 15, 2017, at 5:44 PM, Kathryn Spencer <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi all;
>                Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
>                Thanks so much.
>                Kathy Spencer
>
>
> The Scripps Research Institute
> Dept of Molecular and Cellular Neuroscience
> 10550 N. Torrey Pines Road
> DNC 216
> La Jolla, Ca 92037
Sven Terclavers-3 Sven Terclavers-3
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

In reply to this post by Kathryn Spencer
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

***commercial response***

Dear Kathryn,

ZEISS Microscopy has such a similar setup in  France, though there they use the system for plant imaging. It does function completely automated thanks to a robotic structure. If you're interested in knowing more about this system, I can send you a personal email introducing you to the 3D Imaging Specialist who helped developing this customized solution. Let me know!
Best regards,

Sven Terclavers

Embedded 3D Imaging Specialist at Harvard Center for Biological Imaging
ZEISS Microscopy

Sent from my iPhone

> On Jun 15, 2017, at 17:44, Kathryn Spencer <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi all;
>                Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
>                Thanks so much.
>                Kathy Spencer
>
>
> The Scripps Research Institute
> Dept of Molecular and Cellular Neuroscience
> 10550 N. Torrey Pines Road
> DNC 216
> La Jolla, Ca 92037
Nicholas Reder Nicholas Reder
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

3Scan, based out of San Francisco, may also be of interest: www.3scan.com

Nicholas Reder
Sent from my iPhone

On Jun 15, 2017, 3:48 PM -0700, Sven Terclavers <[hidden email]>, wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> ***commercial response***
>
> Dear Kathryn,
>
> ZEISS Microscopy has such a similar setup in France, though there they use the system for plant imaging. It does function completely automated thanks to a robotic structure. If you're interested in knowing more about this system, I can send you a personal email introducing you to the 3D Imaging Specialist who helped developing this customized solution. Let me know!
> Best regards,
>
> Sven Terclavers
>
> Embedded 3D Imaging Specialist at Harvard Center for Biological Imaging
> ZEISS Microscopy
>
> Sent from my iPhone
>
> > On Jun 15, 2017, at 17:44, Kathryn Spencer <[hidden email]> wrote:
> >
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > Post images on http://www.imgur.com and include the link in your posting.
> > *****
> >
> > Hi all;
> > Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
> > Thanks so much.
> > Kathy Spencer
> >
> >
> > The Scripps Research Institute
> > Dept of Molecular and Cellular Neuroscience
> > 10550 N. Torrey Pines Road
> > DNC 216
> > La Jolla, Ca 92037
Tim Feinstein Tim Feinstein
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

In reply to this post by Kathryn Spencer
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Kathryn,

My group has used those for a while:

https://www.jci.org/articles/view/33284

However our approach is apparently unique.  We have a bespoke design based on a Leica SM2500 microtome with an upright confocal mounted on top.  It uses a 1x lens to capture autofluorescence and build a 3D map of paraffin-embedded embryos before histo staining the sections.  

I did not know commercial options exist!  Thanks to others for pointing them out.  Episcopic serial sectioning has become very important to our work.  
       
Best,


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Kathryn Spencer
Sent: Thursday, June 15, 2017 5:44 PM
To: [hidden email]
Subject: Serial block face sectioning with confocal/multiphoton imaging

*****
To join, leave or search the confocal microscopy listserv, go to:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=01%7C01%7Ctnf8%40PITT.EDU%7C897421d5d2fa497229d908d4b439fe42%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=a4494zElyC6c89NbI9O9vQbVXygYT1HylSAjJTNT%2FJE%3D&reserved=0
Post images on https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=01%7C01%7Ctnf8%40PITT.EDU%7C897421d5d2fa497229d908d4b439fe42%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zG7VjzzXGunZvooHV49%2BFa7N7ZNPs9wIa1FfEpysBPE%3D&reserved=0 and include the link in your posting.
*****

Hi all;
                Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
                Thanks so much.
                Kathy Spencer


The Scripps Research Institute
Dept of Molecular and Cellular Neuroscience
10550 N. Torrey Pines Road
DNC 216
La Jolla, Ca 92037
Rusty Nicovich Rusty Nicovich
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

My group runs 6 of the TissueCyte systems with a new mouse brain daily.
Being serial 2-photon imaging systems there is a trade-off between scanning
speed and resolution (or really, sampling and speed).  Still the
researchers here are quite happy with the quality of the data that comes
off of these systems.  Happy to discuss details if this is something of
interest.

Thanks,
Rusty Nicovich

On Thu, Jun 15, 2017 at 4:47 PM, Feinstein, Timothy N <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Kathryn,
>
> My group has used those for a while:
>
> https://www.jci.org/articles/view/33284
>
> However our approach is apparently unique.  We have a bespoke design based
> on a Leica SM2500 microtome with an upright confocal mounted on top.  It
> uses a 1x lens to capture autofluorescence and build a 3D map of
> paraffin-embedded embryos before histo staining the sections.
>
> I did not know commercial options exist!  Thanks to others for pointing
> them out.  Episcopic serial sectioning has become very important to our
> work.
>
> Best,
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> Research Scientist
> University of Pittsburgh Department of Developmental Biology
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Kathryn Spencer
> Sent: Thursday, June 15, 2017 5:44 PM
> To: [hidden email]
> Subject: Serial block face sectioning with confocal/multiphoton imaging
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%
> 3Dconfocalmicroscopy&data=01%7C01%7Ctnf8%40PITT.EDU%
> 7C897421d5d2fa497229d908d4b439fe42%7C9ef9f489e0a04eeb87cc3a526112
> fd0d%7C1&sdata=a4494zElyC6c89NbI9O9vQbVXygYT1HylSAjJTNT%2FJE%3D&reserved=0
> Post images on https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Fwww.imgur.com&data=01%7C01%7Ctnf8%40PITT.EDU%
> 7C897421d5d2fa497229d908d4b439fe42%7C9ef9f489e0a04eeb87cc3a526112
> fd0d%7C1&sdata=zG7VjzzXGunZvooHV49%2BFa7N7ZNPs9wIa1FfEpysBPE%3D&reserved=0
> and include the link in your posting.
> *****
>
> Hi all;
>                 Can you tell me about any commercial systems that will do
> block-face confocal or multiphoton imaging, slice off a tissue section,
> then reimage the newly exposed surface? And reconstruct the volume? We'd
> like to do this with mouse brains and embryos with endogenous proteins. The
> goal is to have higher resolution than we can get with clearing and
> light-sheet microscopy.
>                 Thanks so much.
>                 Kathy Spencer
>
>
> The Scripps Research Institute
> Dept of Molecular and Cellular Neuroscience
> 10550 N. Torrey Pines Road
> DNC 216
> La Jolla, Ca 92037
>
Oliver Biehlmaier-2 Oliver Biehlmaier-2
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

In reply to this post by Kathryn Spencer
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Kathy,

We are running a TissueCyte1000 at our facility since approx. 3 years and are using it for various types of samples like brain, kidney, spleen, liver, etc.
Once setup the system runs nicely (24/7) and stably, however - like with many of the systems that generate huge amounts of data -  be aware that setting up a data handling and image analysis workflow for various types of samples is quite a challenge. Altogether, the latter, as well as user introduction to the system are taking up quite some time of facility staff, in particular, if you have many users with many different samples…...

Best,
Oliver



Oliver Biehlmaier, PhD | Head of Imaging Core Facility  | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
Phone: +41 61 207 20 73 | Email: [hidden email]<mailto:[hidden email]> | www.biozentrum.unibas.ch/imcf<http://www.biozentrum.unibas.ch/imcf> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>








On 15 Jun 2017, at 23:44, Kathryn Spencer <[hidden email]<mailto:[hidden email]>> wrote:

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi all;
               Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
               Thanks so much.
               Kathy Spencer


The Scripps Research Institute
Dept of Molecular and Cellular Neuroscience
10550 N. Torrey Pines Road
DNC 216
La Jolla, Ca 92037

Julio Mateos Langerak Julio Mateos Langerak
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

In reply to this post by Sven Terclavers-3
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Kathy,

The system mentioned from Zeiss is at our facility (Montpellier Ressources Imagerie).

http://www.mri.cnrs.fr/en/optical-imaging/our-facilities/178-mri-phiv/equipements-phiv-lavalette-2/multiphotonic-microscopy/246-droit-zeiss-880-laser-coherent-chameleon-ultra-ii.html

You may contact Geneviève Conéjéro or Marc Lartaud if you want details on it from our side.

Best, Julio


Sent from my iPhone

> On 16 Jun 2017, at 00:48, Sven Terclavers <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> ***commercial response***
>
> Dear Kathryn,
>
> ZEISS Microscopy has such a similar setup in  France, though there they use the system for plant imaging. It does function completely automated thanks to a robotic structure. If you're interested in knowing more about this system, I can send you a personal email introducing you to the 3D Imaging Specialist who helped developing this customized solution. Let me know!
> Best regards,
>
> Sven Terclavers
>
> Embedded 3D Imaging Specialist at Harvard Center for Biological Imaging
> ZEISS Microscopy
>
> Sent from my iPhone
>
>> On Jun 15, 2017, at 17:44, Kathryn Spencer <[hidden email]> wrote:
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Hi all;
>>              Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
>>              Thanks so much.
>>              Kathy Spencer
>>
>>
>> The Scripps Research Institute
>> Dept of Molecular and Cellular Neuroscience
>> 10550 N. Torrey Pines Road
>> DNC 216
>> La Jolla, Ca 92037
Denise Ramirez Denise Ramirez
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

In reply to this post by Kathryn Spencer
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Kathryn -

We operate two Tissuevision TissueCyte 1000 serial two-photon microscopes on a fee-for-service basis in our core facility and we accept external client samples. The system is ideal for high-resolution volumetric imaging of transgenically or virally labeled whole organ specimens. Please visit our website (http://www.utsouthwestern.edu/education/medical-school/departments/neurology/research/microscopy-facility/) for more information and feel free to contact me with any questions you may have.

Best regards,
Denise

Denise M. Ramirez, Ph.D.
Core Manager, Whole Brain Microscopy Facility
Assistant Professor, Department of Neurology and Neurotherapeutics
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390-8813
214-648-0203
Tim Feinstein Tim Feinstein
Reply | Threaded
Open this post in threaded view
|

Re: Serial block face sectioning with confocal/multiphoton imaging

In reply to this post by Kathryn Spencer
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi folks,

Following up on this question, our block face macro-confocal depends on a Leica SM2500 microtome.  We could use a spare in case of trouble, but Leica stopped selling SM2500’s or even spare parts and eBay only rarely has those.  

If anyone knows of a SM2500 that the owner is willing to sell or pass on, we would be quite grateful.  Non-working is fine since we could use it for parts.  

Many thanks!


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology


On 6/15/17, 5:44 PM, "Confocal Microscopy List on behalf of Kathryn Spencer" <[hidden email] on behalf of [hidden email]> wrote:

    *****
    To join, leave or search the confocal microscopy listserv, go to:
    https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&data=01%7C01%7Ctnf8%40PITT.EDU%7C897421d5d2fa497229d908d4b439fe42%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=a4494zElyC6c89NbI9O9vQbVXygYT1HylSAjJTNT%2FJE%3D&reserved=0
    Post images on https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com&data=01%7C01%7Ctnf8%40PITT.EDU%7C897421d5d2fa497229d908d4b439fe42%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=zG7VjzzXGunZvooHV49%2BFa7N7ZNPs9wIa1FfEpysBPE%3D&reserved=0 and include the link in your posting.
    *****
   
    Hi all;
                    Can you tell me about any commercial systems that will do block-face confocal or multiphoton imaging, slice off a tissue section, then reimage the newly exposed surface? And reconstruct the volume? We'd like to do this with mouse brains and embryos with endogenous proteins. The goal is to have higher resolution than we can get with clearing and light-sheet microscopy.
                    Thanks so much.
                    Kathy Spencer
   
   
    The Scripps Research Institute
    Dept of Molecular and Cellular Neuroscience
    10550 N. Torrey Pines Road
    DNC 216
    La Jolla, Ca 92037