Light sheet fluorescence microscopy

[Nicola Green]

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Hi
This is not strictly confocal microscopy, but I hope you might be able to
help still.
I am interested in using the light sheet fluorescence/single plane
illumination microscopy technique for imaging live 3D tissue engineered
constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
Has anyone had any experience with using this and can comment on it or do
you know of any other similar commercially available systems?
I know that many people report building their own systems but I am not
thinking to go down that route at the moment.
Thanks for your help
Regards
Nicola

[phil laissue-2]

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Hi Nicola,
I'll get to test the Z1 at the end of the month and can let you know
afterwards, also comparing it to the custom system I use. What kind of
tissue do you want to look at?
Kind regards
Philippe
_____________________________________
Philippe Laissue, PhD, Bioimaging Manager
School of Biological Sciences, Room 4.17
University of Essex, Colchester CO4 3SQ, UK
(0044) 01206 872246 / (0044) 07842 676 456
[hidden email]
privatewww.essex.ac.uk/~plaissue


On Tue, Jun 4, 2013 at 10:13 AM, Nicola Green <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi
> This is not strictly confocal microscopy, but I hope you might be able to
> help still.
> I am interested in using the light sheet fluorescence/single plane
> illumination microscopy technique for imaging live 3D tissue engineered
> constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
> Has anyone had any experience with using this and can comment on it or do
> you know of any other similar commercially available systems?
> I know that many people report building their own systems but I am not
> thinking to go down that route at the moment.
> Thanks for your help
> Regards
> Nicola

[George McNamara]

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Hi Nicola,

LaVision Biotec sells the "Ultramicroscope". Former colleagues at UMiami
told me this instrument is giving them excellent images of YFP
expressing neurons (in a subset of cells) of the entire mouse brains in
3 minutes at 1 um 'resolution' (they may mean pixel size). They have
improved on the Erturk ... Dodt et al recipe:

1: Ertürk A, Becker K, Jährling N, Mauch CP, Hojer CD, Egen JG, Hellal F, Bradke
F, Sheng M, Dodt HU. Three-dimensional imaging of solvent-cleared organs using
3DISCO. Nat Protoc. 2012 Nov;7(11):1983-95. doi: 10.1038/nprot.2012.119. Epub
2012 Oct 11. PubMed PMID: 23060243.


2: Ertürk A, Mauch CP, Hellal F, Förstner F, Keck T, Becker K, Jährling N,
Steffens H, Richter M, Hübener M, Kramer E, Kirchhoff F, Dodt HU, Bradke F.
Three-dimensional imaging of the unsectioned adult spinal cord to assess axon
regeneration and glial responses after injury. Nat Med. 2011 Dec 25;18(1):166-71.
doi: 10.1038/nm.2600. PubMed PMID: 22198277.


which they find works better than Scale. See:

Luo X, Salgueiro Y, Beckerman SR, Lemmon VP, Tsoulfas P, Park KK.
Three-dimensional evaluation of retinal ganglion cell axon regeneration
and pathfinding in whole mouse tissue after injury. Exp Neurol. 2013 Mar
16. doi:pii: S0014-4886(13)00084-8. 10.1016/j.expneurol.2013.03.001.
[Epub ahead of print] PubMed PMID: 23510761.


As for focusing only on current commercial systems: big mistake.

See http://www.focusonmicroscopy.org/2013/index.html   for lots of
activity in this field, and especially

Wu and Shroff dual view isotropic 330 nm resolution (with 20x/0.8 NA
lenses and clever image processing)

http://www.focusonmicroscopy.org/2013/PDF/159_Shroff.pdf


George

On 6/4/2013 4:13 AM, Nicola Green wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi
> This is not strictly confocal microscopy, but I hope you might be able to
> help still.
> I am interested in using the light sheet fluorescence/single plane
> illumination microscopy technique for imaging live 3D tissue engineered
> constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
> Has anyone had any experience with using this and can comment on it or do
> you know of any other similar commercially available systems?
> I know that many people report building their own systems but I am not
> thinking to go down that route at the moment.
> Thanks for your help
> Regards
> Nicola
>
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054

[Johannes Schindelin]

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Hi George & Nicola,

On Tue, 4 Jun 2013, George McNamara wrote:

> On 6/4/2013 4:13 AM, Nicola Green wrote:
> >
> > I am interested in using the light sheet fluorescence/single plane
> > illumination microscopy technique for imaging live 3D tissue engineered
> > constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
> > Has anyone had any experience with using this and can comment on it or do
> > you know of any other similar commercially available systems?
> >
> > I know that many people report building their own systems but I am not
> > thinking to go down that route at the moment.
>
> [...]
>
> As for focusing only on current commercial systems: big mistake.
>
> See http://www.focusonmicroscopy.org/2013/index.html   for lots of
> activity in this field, and especially
>
> Wu and Shroff dual view isotropic 330 nm resolution (with 20x/0.8 NA lenses
> and clever image processing)
>
> http://www.focusonmicroscopy.org/2013/PDF/159_Shroff.pdf

Interesting. A (not all too) quick web search found no details about the
setup, just beautiful images.

I would like to point to a project I am personally involved in (together
with a couple of other list regulars) and whose focus is primarily to make
light-sheet microscopy accessible: http://openspim.org/. It contains a
detailed parts list and instructions how to build it even if you are not
an optics expert, along with fully Open Source control software.

The key to the OpenSPIM is that it is an accessible platform, i.e. it can
be extended and enhanced very easily.

For example, I imagine that once information about Wu and Shroff's dual
view setup becomes available, someone will come up with minimal
modifications to the OpenSPIM setup to replicate the same results, and for
maximal impact that someone could extend http://openspim.org/ (which is a
Wiki) to describe those modifications so that other people can easily
rebuild that setup, too.

Ciao,
Johannes

[Johannes Schindelin]

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Hi,

On Tue, 4 Jun 2013, Johannes Schindelin wrote:

> On Tue, 4 Jun 2013, George McNamara wrote:
>
> > On 6/4/2013 4:13 AM, Nicola Green wrote:
> > >
> > > I am interested in using the light sheet fluorescence/single plane
> > > illumination microscopy technique for imaging live 3D tissue
> > > engineered constructs. I know that Zeiss sell the Lightsheet Z1
> > > system that does this.  Has anyone had any experience with using
> > > this and can comment on it or do you know of any other similar
> > > commercially available systems?
> > >
> > > I know that many people report building their own systems but I am
> > > not thinking to go down that route at the moment.
> >
> > [...]
> >
> > As for focusing only on current commercial systems: big mistake.
> >
> > See http://www.focusonmicroscopy.org/2013/index.html   for lots of
> > activity in this field, and especially
> >
> > Wu and Shroff dual view isotropic 330 nm resolution (with 20x/0.8 NA lenses
> > and clever image processing)
> >
> > http://www.focusonmicroscopy.org/2013/PDF/159_Shroff.pdf
>
> Interesting. A (not all too) quick web search found no details about the
> setup, just beautiful images.

There is actually a paper which I found linked from some related NIH page
describing the system:

        http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462167/?report=reader#!po=65.9091

In their Data Processing section, they have a link to the software hosted
on Google Code which actually contains a Wiki where they describe how to
rebuild their setup:

        http://code.google.com/p/msim/wiki/Building_your_own_MSIM

I added a link to http://openspim.org/Links.

Note that in the Deconvolution section of above-linked paper, it is stated
that they use the Parallel Iterative Deconvolution plugin for Image, but
of course they mean ImageJ.

Ciao,
Johannes

[Douglas Richardson]

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Hello Nicola,

Zeiss is currently the only commercial manufacturer of a Lightsheet
system.  We just installed the first system in North America in our
facility, not sure how many have already been installed in Europe.  We're
very impressed with the system.

Feel free to contact me off-list for more details.

-Doug

http://labs.mcb.harvard.edu/hcbi/


On Tue, Jun 4, 2013 at 5:13 AM, Nicola Green <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi
> This is not strictly confocal microscopy, but I hope you might be able to
> help still.
> I am interested in using the light sheet fluorescence/single plane
> illumination microscopy technique for imaging live 3D tissue engineered
> constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
> Has anyone had any experience with using this and can comment on it or do
> you know of any other similar commercially available systems?
> I know that many people report building their own systems but I am not
> thinking to go down that route at the moment.
> Thanks for your help
> Regards
> Nicola
>

[Dr. Judith Drazba]

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Hi all,

As mentioned earlier today by George McNamara, there are two commercial manufacturers of Lightsheet systems. While the Zeiss Z1 appears to be optimized for very small living samples like zebrafish and drosophila embryos, the LaVision system does a great job on larger samples like whole mouse brain that has been cleared. I've been reviewing them both in anticipation of a purchase later this year.

 Judith Drazba, Ph.D.  |  Director  |  Imaging Core - LRI
 Cleveland Clinic, NB10  |  9500 Euclid Ave.   |  Cleveland, OH 44195 
 [phone]  |  [phone]





-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Douglas Richardson
Sent: Tuesday, June 04, 2013 11:17 AM
To: [hidden email]
Subject: Re: Light sheet fluorescence microscopy

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Hello Nicola,

Zeiss is currently the only commercial manufacturer of a Lightsheet system.  We just installed the first system in North America in our facility, not sure how many have already been installed in Europe.  We're very impressed with the system.

Feel free to contact me off-list for more details.

-Doug

http://labs.mcb.harvard.edu/hcbi/


On Tue, Jun 4, 2013 at 5:13 AM, Nicola Green <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi
> This is not strictly confocal microscopy, but I hope you might be able
> to help still.
> I am interested in using the light sheet fluorescence/single plane
> illumination microscopy technique for imaging live 3D tissue
> engineered constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
> Has anyone had any experience with using this and can comment on it or
> do you know of any other similar commercially available systems?
> I know that many people report building their own systems but I am not
> thinking to go down that route at the moment.
> Thanks for your help
> Regards
> Nicola
>

===================================


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Thank you.

[Raghu Parthasarathy]

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   One commercial light sheet implementation that hasn't been mentioned:  ASI sells the "inverted SPIM" setup that they & Hari Shroff et al. developed (www.pnas.org/cgi/doi/10.1073/pnas.1108494108):  http://www.asiimaging.com/products/light-sheet-microscopy/inverted-selective-plane-illumination-microscopy-ispim/ .

   I haven't used any of the commercial setups; it's fun and not particularly hard to build one's own light sheet microscope.  The OpenSPIM wiki noted in another reply seems quite good, by the way.

best wishes,

Raghu


 
--
Raghuveer Parthasarathy
[hidden email]
Group: http://physics.uoregon.edu/~raghu/
Blog: http://eighteenthelephant.wordpress.com/


Associate Professor
Department of Physics
1274 University of Oregon
Eugene, OR 97403-1274



________________________________
 From: Nicola Green <[hidden email]>
To: [hidden email]
Sent: Tuesday, June 4, 2013 2:13 AM
Subject: Light sheet fluorescence microscopy
 

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

Hi
This is not strictly confocal microscopy, but I hope you might be able to
help still.
I am interested in using the light sheet fluorescence/single plane
illumination microscopy technique for imaging live 3D tissue engineered
constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
Has anyone had any experience with using this and can comment on it or do
you know of any other similar commercially available systems?
I know that many people report building their own systems but I am not
thinking to go down that route at the moment.
Thanks for your help
Regards
Nicola

[Nuno Moreno]

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Hi,

For micromanager and open source hardware fans please have a look at this DSLM/SPIM/OPT configuration

https://sites.google.com/site/openspinmicroscopy/

Coming on nature methods (july issue) as correspondence.

This system uses arduino boards and a custom build micromanager interface for dealing with sample rotation, galvo-speed, timelapse, etc, etc. Using this methodology you can setup a "spin" microscope for less than 50k euros even with topnotch camera and objective.

Best,
Nuno Moreno, PhD
Instituto Gulbenkian de Ciência
http://lnkd.in/6VXcrM





On Jun 4, 2013, at 4:16 PM, Douglas Richardson wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello Nicola,
>
> Zeiss is currently the only commercial manufacturer of a Lightsheet
> system.  We just installed the first system in North America in our
> facility, not sure how many have already been installed in Europe.  We're
> very impressed with the system.
>
> Feel free to contact me off-list for more details.
>
> -Doug
>
> http://labs.mcb.harvard.edu/hcbi/
>
>
> On Tue, Jun 4, 2013 at 5:13 AM, Nicola Green <[hidden email]>wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Hi
>> This is not strictly confocal microscopy, but I hope you might be able to
>> help still.
>> I am interested in using the light sheet fluorescence/single plane
>> illumination microscopy technique for imaging live 3D tissue engineered
>> constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
>> Has anyone had any experience with using this and can comment on it or do
>> you know of any other similar commercially available systems?
>> I know that many people report building their own systems but I am not
>> thinking to go down that route at the moment.
>> Thanks for your help
>> Regards
>> Nicola
>>

[Douglas Richardson]

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

Just wanted to apologize for my earlier post.  When I stated the Z1 was the
only commercial implementation of a lightsheet microscope I was just
  referring to the big 4 (Zeiss/Leica/Nikon/Olympus). As indicated by other
posts, other commercial implementations exist.

Sorry for the confusion,

-Doug


On Tue, Jun 4, 2013 at 12:29 PM, Nuno Moreno <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi,
>
> For micromanager and open source hardware fans please have a look at this
> DSLM/SPIM/OPT configuration
>
> https://sites.google.com/site/openspinmicroscopy/
>
> Coming on nature methods (july issue) as correspondence.
>
> This system uses arduino boards and a custom build micromanager interface
> for dealing with sample rotation, galvo-speed, timelapse, etc, etc. Using
> this methodology you can setup a "spin" microscope for less than 50k euros
> even with topnotch camera and objective.
>
> Best,
> Nuno Moreno, PhD
> Instituto Gulbenkian de Ciência
> http://lnkd.in/6VXcrM
>
>
>
>
>
> On Jun 4, 2013, at 4:16 PM, Douglas Richardson wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Hello Nicola,
> >
> > Zeiss is currently the only commercial manufacturer of a Lightsheet
> > system.  We just installed the first system in North America in our
> > facility, not sure how many have already been installed in Europe.  We're
> > very impressed with the system.
> >
> > Feel free to contact me off-list for more details.
> >
> > -Doug
> >
> > http://labs.mcb.harvard.edu/hcbi/
> >
> >
> > On Tue, Jun 4, 2013 at 5:13 AM, Nicola Green <[hidden email]
> >wrote:
> >
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> >> *****
> >>
> >> Hi
> >> This is not strictly confocal microscopy, but I hope you might be able
> to
> >> help still.
> >> I am interested in using the light sheet fluorescence/single plane
> >> illumination microscopy technique for imaging live 3D tissue engineered
> >> constructs. I know that Zeiss sell the Lightsheet Z1 system that does
> this.
> >> Has anyone had any experience with using this and can comment on it or
> do
> >> you know of any other similar commercially available systems?
> >> I know that many people report building their own systems but I am not
> >> thinking to go down that route at the moment.
> >> Thanks for your help
> >> Regards
> >> Nicola
> >>
>

[George McNamara]

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Hi Johannes,

Hari Shoff and his lab have a very good track record on making their
plans and code available - see

https://code.google.com/p/msim/

for details of their 2012 MSIM paper (PubMed 22581372 ).

Hopefully the "instant SIM" (another FOM 2013 abstract) and dual view
SPIM will be published soon (Nature Methods?) and the computational
explanation will be explained and code - and program - made available.
You could always email or call Hari to find out what they did for dual
view SPIM to make it isotropic.

George



On 6/4/2013 9:25 AM, Johannes Schindelin wrote:

> Hi George&  Nicola,
>
> On Tue, 4 Jun 2013, George McNamara wrote:
>
>    
>> On 6/4/2013 4:13 AM, Nicola Green wrote:
>>      
>>> I am interested in using the light sheet fluorescence/single plane
>>> illumination microscopy technique for imaging live 3D tissue engineered
>>> constructs. I know that Zeiss sell the Lightsheet Z1 system that does this.
>>> Has anyone had any experience with using this and can comment on it or do
>>> you know of any other similar commercially available systems?
>>>
>>> I know that many people report building their own systems but I am not
>>> thinking to go down that route at the moment.
>>>        
>> [...]
>>
>> As for focusing only on current commercial systems: big mistake.
>>
>> See http://www.focusonmicroscopy.org/2013/index.html   for lots of
>> activity in this field, and especially
>>
>> Wu and Shroff dual view isotropic 330 nm resolution (with 20x/0.8 NA lenses
>> and clever image processing)
>>
>> http://www.focusonmicroscopy.org/2013/PDF/159_Shroff.pdf
>>      
> Interesting. A (not all too) quick web search found no details about the
> setup, just beautiful images.
>
> I would like to point to a project I am personally involved in (together
> with a couple of other list regulars) and whose focus is primarily to make
> light-sheet microscopy accessible: http://openspim.org/. It contains a
> detailed parts list and instructions how to build it even if you are not
> an optics expert, along with fully Open Source control software.
>
> The key to the OpenSPIM is that it is an accessible platform, i.e. it can
> be extended and enhanced very easily.
>
> For example, I imagine that once information about Wu and Shroff's dual
> view setup becomes available, someone will come up with minimal
> modifications to the OpenSPIM setup to replicate the same results, and for
> maximal impact that someone could extend http://openspim.org/ (which is a
> Wiki) to describe those modifications so that other people can easily
> rebuild that setup, too.
>
> Ciao,
> Johannes
>
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054

[Johannes Schindelin]

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Hi George,

On Tue, 4 Jun 2013, George McNamara wrote:

> Hari Shoff and his lab have a very good track record on making their plans and
> code available - see
>
> https://code.google.com/p/msim/
>
> for details of their 2012 MSIM paper (PubMed 22581372 ).

Did my reply to myself not go through? I had to dig quite a bit to find
that link, though.

Ciao,
Johannes

[phil laissue-2]

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light sheet microscopy was a main theme at this year's FOM, great to
see it take centre stage, and worth checking out several of the FOM
abstracts for this.
_____________________________________
Philippe Laissue, PhD, Bioimaging Manager
School of Biological Sciences, Room 4.17
University of Essex, Colchester CO4 3SQ, UK
(0044) 01206 872246 / (0044) 07842 676 456
[hidden email]
privatewww.essex.ac.uk/~plaissue


On Wed, Jun 5, 2013 at 1:19 AM, George McNamara
<[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Johannes,
>
> Hari Shoff and his lab have a very good track record on making their plans
> and code available - see
>
> https://code.google.com/p/msim/
>
> for details of their 2012 MSIM paper (PubMed 22581372 ).
>
> Hopefully the "instant SIM" (another FOM 2013 abstract) and dual view SPIM
> will be published soon (Nature Methods?) and the computational explanation
> will be explained and code - and program - made available. You could always
> email or call Hari to find out what they did for dual view SPIM to make it
> isotropic.
>
> George
>
>
>
> On 6/4/2013 9:25 AM, Johannes Schindelin wrote:
>>
>> Hi George&  Nicola,
>>
>> On Tue, 4 Jun 2013, George McNamara wrote:
>>
>>
>>>
>>> On 6/4/2013 4:13 AM, Nicola Green wrote:
>>>
>>>>
>>>> I am interested in using the light sheet fluorescence/single plane
>>>> illumination microscopy technique for imaging live 3D tissue engineered
>>>> constructs. I know that Zeiss sell the Lightsheet Z1 system that does
>>>> this.
>>>> Has anyone had any experience with using this and can comment on it or
>>>> do
>>>> you know of any other similar commercially available systems?
>>>>
>>>> I know that many people report building their own systems but I am not
>>>> thinking to go down that route at the moment.
>>>>
>>>
>>> [...]
>>>
>>> As for focusing only on current commercial systems: big mistake.
>>>
>>> See http://www.focusonmicroscopy.org/2013/index.html   for lots of
>>> activity in this field, and especially
>>>
>>> Wu and Shroff dual view isotropic 330 nm resolution (with 20x/0.8 NA
>>> lenses
>>> and clever image processing)
>>>
>>> http://www.focusonmicroscopy.org/2013/PDF/159_Shroff.pdf
>>>
>>
>> Interesting. A (not all too) quick web search found no details about the
>> setup, just beautiful images.
>>
>> I would like to point to a project I am personally involved in (together
>> with a couple of other list regulars) and whose focus is primarily to make
>> light-sheet microscopy accessible: http://openspim.org/. It contains a
>> detailed parts list and instructions how to build it even if you are not
>> an optics expert, along with fully Open Source control software.
>>
>> The key to the OpenSPIM is that it is an accessible platform, i.e. it can
>> be extended and enhanced very easily.
>>
>> For example, I imagine that once information about Wu and Shroff's dual
>> view setup becomes available, someone will come up with minimal
>> modifications to the OpenSPIM setup to replicate the same results, and for
>> maximal impact that someone could extend http://openspim.org/ (which is a
>> Wiki) to describe those modifications so that other people can easily
>> rebuild that setup, too.
>>
>> Ciao,
>> Johannes
>>
>>
>
>
>
> --
>
>
>
> George McNamara, Ph.D.
> Single Cells Analyst
> L.J.N. Cooper Lab
> University of Texas M.D. Anderson Cancer Center
> Houston, TX 77054

[Peter Gabriel Pitrone]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hello Listers,

I thought I would bring to your attention two correspondences in Nature Methods on light sheet
microscopy...

http://www.nature.com/nmeth/journal/vaop/ncurrent/index.html

Have a great work week!!

Pete

--
Peter Gabriel Pitrone - TechRMS
Microscopy/Imaging Specialist
Prof. Dr. Pavel Tomancak group
Max Planck Institute for
Molecular Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden

"If a straight line fit is required, obtain only two data points." - Anon.


On Wed, June 5, 2013 5:08 am, phil laissue wrote:
<|> *****
<|> To join, leave or search the confocal microscopy listserv, go to:
<|> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
<|> *****
<|>
<|> light sheet microscopy was a main theme at this year's FOM, great to
<|> see it take centre stage, and worth checking out several of the FOM
<|> abstracts for this.
<|> _____________________________________
<|> Philippe Laissue, PhD, Bioimaging Manager
<|> School of Biological Sciences, Room 4.17
<|> University of Essex, Colchester CO4 3SQ, UK
<|> (0044) 01206 872246 / (0044) 07842 676 456
<|> [hidden email]
<|> privatewww.essex.ac.uk/~plaissue
<|>
<|>
<|> On Wed, Jun 5, 2013 at 1:19 AM, George McNamara
<|> <[hidden email]> wrote:
<|>> *****
<|>> To join, leave or search the confocal microscopy listserv, go to:
<|>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
<|>> *****
<|>>
<|>> Hi Johannes,
<|>>
<|>> Hari Shoff and his lab have a very good track record on making their plans
<|>> and code available - see
<|>>
<|>> https://code.google.com/p/msim/
<|>>
<|>> for details of their 2012 MSIM paper (PubMed 22581372 ).
<|>>
<|>> Hopefully the "instant SIM" (another FOM 2013 abstract) and dual view SPIM
<|>> will be published soon (Nature Methods?) and the computational explanation
<|>> will be explained and code - and program - made available. You could always
<|>> email or call Hari to find out what they did for dual view SPIM to make it
<|>> isotropic.
<|>>
<|>> George
<|>>
<|>>
<|>>
<|>> On 6/4/2013 9:25 AM, Johannes Schindelin wrote:
<|>>>
<|>>> Hi George&  Nicola,
<|>>>
<|>>> On Tue, 4 Jun 2013, George McNamara wrote:
<|>>>
<|>>>
<|>>>>
<|>>>> On 6/4/2013 4:13 AM, Nicola Green wrote:
<|>>>>
<|>>>>>
<|>>>>> I am interested in using the light sheet fluorescence/single plane
<|>>>>> illumination microscopy technique for imaging live 3D tissue engineered
<|>>>>> constructs. I know that Zeiss sell the Lightsheet Z1 system that does
<|>>>>> this.
<|>>>>> Has anyone had any experience with using this and can comment on it or
<|>>>>> do
<|>>>>> you know of any other similar commercially available systems?
<|>>>>>
<|>>>>> I know that many people report building their own systems but I am not
<|>>>>> thinking to go down that route at the moment.
<|>>>>>
<|>>>>
<|>>>> [...]
<|>>>>
<|>>>> As for focusing only on current commercial systems: big mistake.
<|>>>>
<|>>>> See http://www.focusonmicroscopy.org/2013/index.html   for lots of
<|>>>> activity in this field, and especially
<|>>>>
<|>>>> Wu and Shroff dual view isotropic 330 nm resolution (with 20x/0.8 NA
<|>>>> lenses
<|>>>> and clever image processing)
<|>>>>
<|>>>> http://www.focusonmicroscopy.org/2013/PDF/159_Shroff.pdf
<|>>>>
<|>>>
<|>>> Interesting. A (not all too) quick web search found no details about the
<|>>> setup, just beautiful images.
<|>>>
<|>>> I would like to point to a project I am personally involved in (together
<|>>> with a couple of other list regulars) and whose focus is primarily to make
<|>>> light-sheet microscopy accessible: http://openspim.org/. It contains a
<|>>> detailed parts list and instructions how to build it even if you are not
<|>>> an optics expert, along with fully Open Source control software.
<|>>>
<|>>> The key to the OpenSPIM is that it is an accessible platform, i.e. it can
<|>>> be extended and enhanced very easily.
<|>>>
<|>>> For example, I imagine that once information about Wu and Shroff's dual
<|>>> view setup becomes available, someone will come up with minimal
<|>>> modifications to the OpenSPIM setup to replicate the same results, and for
<|>>> maximal impact that someone could extend http://openspim.org/ (which is a
<|>>> Wiki) to describe those modifications so that other people can easily
<|>>> rebuild that setup, too.
<|>>>
<|>>> Ciao,
<|>>> Johannes
<|>>>
<|>>>
<|>>
<|>>
<|>>
<|>> --
<|>>
<|>>
<|>>
<|>> George McNamara, Ph.D.
<|>> Single Cells Analyst
<|>> L.J.N. Cooper Lab
<|>> University of Texas M.D. Anderson Cancer Center
<|>> Houston, TX 77054
<|>