vibration criteria for super-resolution

[Kate Luby-Phelps]

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I am interested people's practical experience regarding the level of vibration
isolation required for single molecule imaging and super-resolution imaging.

Specifically,  our new building has a z-axis vibration spike that reaches VC-A at
a single frequency (below VC-C in x,y and z for all other frequencies).  If they
are unsuccessful at remediating the spike, would we need active air tables for
high-end instruments?   Most of the scopes in question would be inverted.

Putting the question another way, would we need to reach VC-E or lower for
single molecule and super-resolution imaging?

Thanks,

Kate L-P

[David Baddeley]

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I haven't heard of the VC levels before, but I would think an air table to be necessary for super-resolution work in all but a very, very stable basement. A good approximation is that you will want about the same level of vibration isolation as for electron microscopy (VC-D on a quick google, although if you go by lithographic feature size you'd want VC-E or better). That said, you can probably get away with somewhat higher levels of vibration if it is sufficiently fast (several hundred Hz or higher) that it averages out over your frame time. Fast vibrations will just decrease your widefield resolution somewhat, a fact that can be compensated for by the localisation. We run our super-resolution setups on air tables and still have some vibration issues related to the fans in the EMCCD cameras (if we just slap them on the side port with no additional damping we get focus oscillations on the order 50-100 nm).

cheers,
David


________________________________
 From: Kate Luby-Phelps <[hidden email]>
To: [hidden email]
Sent: Friday, 8 June 2012 8:18 AM
Subject: vibration criteria for super-resolution
 
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I am interested people's practical experience regarding the level of vibration
isolation required for single molecule imaging and super-resolution imaging.

Specifically,  our new building has a z-axis vibration spike that reaches VC-A at
a single frequency (below VC-C in x,y and z for all other frequencies).  If they
are unsuccessful at remediating the spike, would we need active air tables for
high-end instruments?   Most of the scopes in question would be inverted.

Putting the question another way, would we need to reach VC-E or lower for
single molecule and super-resolution imaging?

Thanks,

Kate L-P

[George McNamara]

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Hi Kate,

Yes. Even high resolution confocal microscopes benefit from a serious
air table. Thick table, big legs. Table somewhat larger area than
absolutely necessary. For the STED proposals we submitted last September
(my thanks to the NIH S10 HEI and DoD DURIP reviewers for any nice
comments), TMC table, 300 mm thick, Gimbal piston isolators (aka "fat
legs"), 2x2 meter table (two 2x1 meter modules, to be joined  on site).  
The table Leica shipped in for the CW-STED demo was a joke (see 2009
table thinness at
http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/innovation/ 
).

As David pointed out, you should still plan to register the data.

On the positive side, my Leica confocal/STED salesperson told me good
things about the new model:

http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-tcs-sp8-sted/ 


though I am baffled why Leica is pushing a CW depletion laser(s) with
time gated detection.

Also odd that they have no connection between "STED" and "SMD"

http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-tcs-sp8-smd/


I am curious to see how much (if at all) motCORR helps my users
(assuming we ever find money for upgrade or trade-in)

http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-motcorr/

George
p.s. I have STED proposal stuff posted at
http://works.bepress.com/gmcnamara/3/
http://works.bepress.com/gmcnamara/13/

See also the new Ikataki and Bokor fluorescence depletion paper at  
http://dx.doi.org/10.1016/j.optcom.2012.04.028
and    
http://projectreporter.nih.gov/project_info_description.cfm?aid=8344866&icde=12760271&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC 


Not nanoscopy, but I hope anyone who has - or is thinking of buying - a
Leica FDC495 color camera will find useful the web page text and
download tips at
http://works.bepress.com/gmcnamara/17/
If someone knows a (software only please) "Leica hack" to adjust the
dark current so that the camera reads above zero intensity level (at
gain of 1, gamma of 1, saturation 1, and exposure time <2 seconds) - say
something like the Canon Hack Development Kit whose URL was recently
posted (thanks to whoever did that) - would be great.


On 6/7/2012 4:18 PM, Kate Luby-Phelps wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I am interested people's practical experience regarding the level of vibration
> isolation required for single molecule imaging and super-resolution imaging.
>
> Specifically,  our new building has a z-axis vibration spike that reaches VC-A at
> a single frequency (below VC-C in x,y and z for all other frequencies).  If they
> are unsuccessful at remediating the spike, would we need active air tables for
> high-end instruments?   Most of the scopes in question would be inverted.
>
> Putting the question another way, would we need to reach VC-E or lower for
> single molecule and super-resolution imaging?
>
> Thanks,
>
> Kate L-P
>
>    

[Craig Brideau]

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

I find table thickness to have some pros and cons.  A really thick table
will react slowly to any bumps, or people leaning on it, due to its mass.
 I find smaller individual microscope tables with the 2" thick tops allow
the `scope to bob around a bit too much if somebody bumps it.  You can set
your dampers to reduce this depending on the table design, but generally a
thicker, heavier table responds more 'patiently' to any perturbations.  The
drawback is that for thick tables you can't put your legs underneath.  I
mean the operators's legs, i.e. the poor person who has to sit at the
microscope.  We have 18" thick tables in our labs so using the eyepieces
for any long period of time would probably be uncomfortable: You can't
'sit' at it because there is no room for your legs underneath.  The good
news for us was we use laser scanning scopes, so the eyepieces are used
only to focus on the sample initially then everything is done via the
computer.  You can get a 4" top for small microscope tables that can be a
good compromise for individual rigs, but it depends on how much damping you
need overall and operator comfort tends to get pushed to the bottom of the
priorities list.

Craig




On Thu, Jun 7, 2012 at 6:13 PM, 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<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> *****
>
> Hi Kate,
>
> Yes. Even high resolution confocal microscopes benefit from a serious air
> table. Thick table, big legs. Table somewhat larger area than absolutely
> necessary. For the STED proposals we submitted last September (my thanks to
> the NIH S10 HEI and DoD DURIP reviewers for any nice comments), TMC table,
> 300 mm thick, Gimbal piston isolators (aka "fat legs"), 2x2 meter table
> (two 2x1 meter modules, to be joined  on site).  The table Leica shipped in
> for the CW-STED demo was a joke (see 2009 table thinness at
> http://www.leica-microsystems.**com/products/confocal-**
> microscopes/configurable-**confocal-leica-tcs-sp8/**innovation/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/innovation/> ).
>
> As David pointed out, you should still plan to register the data.
>
> On the positive side, my Leica confocal/STED salesperson told me good
> things about the new model:
>
> http://www.leica-microsystems.**com/products/confocal-**
> microscopes/configurable-**confocal-leica-tcs-sp8/**
> details/product/leica-tcs-sp8-**sted/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-tcs-sp8-sted/>
>
> though I am baffled why Leica is pushing a CW depletion laser(s) with time
> gated detection.
>
> Also odd that they have no connection between "STED" and "SMD"
>
> http://www.leica-microsystems.**com/products/confocal-**
> microscopes/configurable-**confocal-leica-tcs-sp8/**
> details/product/leica-tcs-sp8-**smd/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-tcs-sp8-smd/>
>
>
> I am curious to see how much (if at all) motCORR helps my users (assuming
> we ever find money for upgrade or trade-in)
>
> http://www.leica-microsystems.**com/products/confocal-**
> microscopes/configurable-**confocal-leica-tcs-sp8/**
> details/product/leica-motcorr/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-motcorr/>
>
> George
> p.s. I have STED proposal stuff posted at
> http://works.bepress.com/**gmcnamara/3/<http://works.bepress.com/gmcnamara/3/>
> http://works.bepress.com/**gmcnamara/13/<http://works.bepress.com/gmcnamara/13/>
>
> See also the new Ikataki and Bokor fluorescence depletion paper at
> http://dx.doi.org/10.1016/j.**optcom.2012.04.028<http://dx.doi.org/10.1016/j.optcom.2012.04.028>
> and     http://projectreporter.nih.**gov/project_info_description.**
> cfm?aid=8344866&icde=12760271&**ddparam=&ddvalue=&ddsub=&cr=3&**
> csb=default&cs=ASC<http://projectreporter.nih.gov/project_info_description.cfm?aid=8344866&icde=12760271&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC>
>
> Not nanoscopy, but I hope anyone who has - or is thinking of buying - a
> Leica FDC495 color camera will find useful the web page text and download
> tips at
> http://works.bepress.com/**gmcnamara/17/<http://works.bepress.com/gmcnamara/17/>
> If someone knows a (software only please) "Leica hack" to adjust the dark
> current so that the camera reads above zero intensity level (at gain of 1,
> gamma of 1, saturation 1, and exposure time <2 seconds) - say something
> like the Canon Hack Development Kit whose URL was recently posted (thanks
> to whoever did that) - would be great.
>
>
>
> On 6/7/2012 4:18 PM, Kate Luby-Phelps 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>
>> *****
>>
>> I am interested people's practical experience regarding the level of
>> vibration
>> isolation required for single molecule imaging and super-resolution
>> imaging.
>>
>> Specifically,  our new building has a z-axis vibration spike that reaches
>> VC-A at
>> a single frequency (below VC-C in x,y and z for all other frequencies).
>>  If they
>> are unsuccessful at remediating the spike, would we need active air
>> tables for
>> high-end instruments?   Most of the scopes in question would be inverted.
>>
>> Putting the question another way, would we need to reach VC-E or lower for
>> single molecule and super-resolution imaging?
>>
>> Thanks,
>>
>> Kate L-P
>>
>>
>>
>

[Kate Luby-Phelps]

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

Thank you for your replies David and George.

The spike is at 18Hz, so would probably have the effect you mentioned of
broadening the widefield resolution. Even though the spike is in z and not lateral,
I think the z vibration will change the width of the PSF and reduce lateral
resolution.

We can probably damp the spike to VC-C with a good passive air table. To get to
VC-D or E we will need an active table. It sounds as if it is worth the significant
extra cost.

Kate

[Mark Cannell]

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

I ordered a thick  table with a leg cut out. Worked well.

Cheers

On 11/06/2012, at 7:51 PM, Craig Brideau wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I find table thickness to have some pros and cons.  A really thick table
> will react slowly to any bumps, or people leaning on it, due to its mass.
> I find smaller individual microscope tables with the 2" thick tops allow
> the `scope to bob around a bit too much if somebody bumps it.  You can set
> your dampers to reduce this depending on the table design, but generally a
> thicker, heavier table responds more 'patiently' to any perturbations.  The
> drawback is that for thick tables you can't put your legs underneath.  I
> mean the operators's legs, i.e. the poor person who has to sit at the
> microscope.  We have 18" thick tables in our labs so using the eyepieces
> for any long period of time would probably be uncomfortable: You can't
> 'sit' at it because there is no room for your legs underneath.  The good
> news for us was we use laser scanning scopes, so the eyepieces are used
> only to focus on the sample initially then everything is done via the
> computer.  You can get a 4" top for small microscope tables that can be a
> good compromise for individual rigs, but it depends on how much damping you
> need overall and operator comfort tends to get pushed to the bottom of the
> priorities list.
>
> Craig
>
>
>
>
> On Thu, Jun 7, 2012 at 6:13 PM, 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<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>> *****
>>
>> Hi Kate,
>>
>> Yes. Even high resolution confocal microscopes benefit from a serious air
>> table. Thick table, big legs. Table somewhat larger area than absolutely
>> necessary. For the STED proposals we submitted last September (my thanks to
>> the NIH S10 HEI and DoD DURIP reviewers for any nice comments), TMC table,
>> 300 mm thick, Gimbal piston isolators (aka "fat legs"), 2x2 meter table
>> (two 2x1 meter modules, to be joined  on site).  The table Leica shipped in
>> for the CW-STED demo was a joke (see 2009 table thinness at
>> http://www.leica-microsystems.**com/products/confocal-**
>> microscopes/configurable-**confocal-leica-tcs-sp8/**innovation/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/innovation/> ).
>>
>> As David pointed out, you should still plan to register the data.
>>
>> On the positive side, my Leica confocal/STED salesperson told me good
>> things about the new model:
>>
>> http://www.leica-microsystems.**com/products/confocal-**
>> microscopes/configurable-**confocal-leica-tcs-sp8/**
>> details/product/leica-tcs-sp8-**sted/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-tcs-sp8-sted/>
>>
>> though I am baffled why Leica is pushing a CW depletion laser(s) with time
>> gated detection.
>>
>> Also odd that they have no connection between "STED" and "SMD"
>>
>> http://www.leica-microsystems.**com/products/confocal-**
>> microscopes/configurable-**confocal-leica-tcs-sp8/**
>> details/product/leica-tcs-sp8-**smd/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-tcs-sp8-smd/>
>>
>>
>> I am curious to see how much (if at all) motCORR helps my users (assuming
>> we ever find money for upgrade or trade-in)
>>
>> http://www.leica-microsystems.**com/products/confocal-**
>> microscopes/configurable-**confocal-leica-tcs-sp8/**
>> details/product/leica-motcorr/<http://www.leica-microsystems.com/products/confocal-microscopes/configurable-confocal-leica-tcs-sp8/details/product/leica-motcorr/>
>>
>> George
>> p.s. I have STED proposal stuff posted at
>> http://works.bepress.com/**gmcnamara/3/<http://works.bepress.com/gmcnamara/3/>
>> http://works.bepress.com/**gmcnamara/13/<http://works.bepress.com/gmcnamara/13/>
>>
>> See also the new Ikataki and Bokor fluorescence depletion paper at
>> http://dx.doi.org/10.1016/j.**optcom.2012.04.028<http://dx.doi.org/10.1016/j.optcom.2012.04.028>
>> and     http://projectreporter.nih.**gov/project_info_description.**
>> cfm?aid=8344866&icde=12760271&**ddparam=&ddvalue=&ddsub=&cr=3&**
>> csb=default&cs=ASC<http://projectreporter.nih.gov/project_info_description.cfm?aid=8344866&icde=12760271&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC>
>>
>> Not nanoscopy, but I hope anyone who has - or is thinking of buying - a
>> Leica FDC495 color camera will find useful the web page text and download
>> tips at
>> http://works.bepress.com/**gmcnamara/17/<http://works.bepress.com/gmcnamara/17/>
>> If someone knows a (software only please) "Leica hack" to adjust the dark
>> current so that the camera reads above zero intensity level (at gain of 1,
>> gamma of 1, saturation 1, and exposure time <2 seconds) - say something
>> like the Canon Hack Development Kit whose URL was recently posted (thanks
>> to whoever did that) - would be great.
>>
>>
>>
>> On 6/7/2012 4:18 PM, Kate Luby-Phelps 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>
>>> *****
>>>
>>> I am interested people's practical experience regarding the level of
>>> vibration
>>> isolation required for single molecule imaging and super-resolution
>>> imaging.
>>>
>>> Specifically,  our new building has a z-axis vibration spike that reaches
>>> VC-A at
>>> a single frequency (below VC-C in x,y and z for all other frequencies).
>>> If they
>>> are unsuccessful at remediating the spike, would we need active air
>>> tables for
>>> high-end instruments?   Most of the scopes in question would be inverted.
>>>
>>> Putting the question another way, would we need to reach VC-E or lower for
>>> single molecule and super-resolution imaging?
>>>
>>> Thanks,
>>>
>>> Kate L-P
>>>
>>>
>>>
>>

[Craig Brideau]

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

That's pretty nifty.  I knew that most table companies will slice all sorts
of notches and the like into their tables, but it never occurred to me to
use this ability to have a leg cut out put in.  How much did it increase
the cost of the table?  Did the company say there would be any significant
change in the table's vibration damping ability?

Craig


On Tue, Jun 12, 2012 at 1:11 AM, Mark Cannell <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I ordered a thick  table with a leg cut out. Worked well.
>
> Cheers
>
>

[Mark Cannell]

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

The cost was not huge but I can't actually remember how much! They said that the cut out would have only minor effects on bending modes and almost no effect on vertical and horizontal modes. Since the table worked well I think they were probably right... The leg cut out was not full thickness abut only half -enough to enable you to get your knees under the table.

Cheers


On 12/06/2012, at 8:20 AM, Craig Brideau wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> That's pretty nifty.  I knew that most table companies will slice all sorts
> of notches and the like into their tables, but it never occurred to me to
> use this ability to have a leg cut out put in.  How much did it increase
> the cost of the table?  Did the company say there would be any significant
> change in the table's vibration damping ability?
>
> Craig
>
>
> On Tue, Jun 12, 2012 at 1:11 AM, Mark Cannell <[hidden email]>wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> I ordered a thick  table with a leg cut out. Worked well.
>>
>> Cheers
>>
>>