Posted by
Jason Brenner on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Re-CONFOCALMICROSCOPY-Digest-25-May-2010-to-26-May-2010-2010-16-tp5107012.html
If you are getting this in the morning, good morning! I love you!
Jason Brenner
Microscope Sales Representative
Olympus America, Inc.
107 Kay Street
Ithaca, NY 14850
Mobile: 607-592-1200
[hidden email]
http://www.olympusamerica.com/seg_section/seg_home.asp----- Original Message -----
From: CONFOCALMICROSCOPY automatic digest system [
[hidden email]]
Sent: 05/27/2010 12:02 AM EST
To:
[hidden email]
Subject: CONFOCALMICROSCOPY Digest - 25 May 2010 to 26 May 2010 (#2010-16)
There are 9 messages totalling 585 lines in this issue.
Topics of the day:
1. colocalization and focus *commercial response*
2. Primary dochroics in A1r
3. Resonant scanner from A1R vs SP5 ...
4. AUTO: Dupal, Mark is out of the office. (returning 28/05/2010)
5. Poor man's confocal (5)
----------------------------------------------------------------------
Date: Wed, 26 May 2010 09:27:29 +0200
From: Daniel James White <
[hidden email]>
Subject: Re: colocalization and focus *commercial response*
Hi Kevin and Carl,
Begin forwarded message:
>=20
> Hi Carl,
>=20
> According to Bitplane's records, there is a permanent license for =
Imaris=20
> 5.5 registered to you.
> Although you can't upgrade it or get support without renewing=20
> maintenance, I'm pretty sure that version has the necessary components=20=
> to apply channel shift corrections.
> The simplest approach would be via the Image Processing menu if Imaris=20=
> ("Channel Shift") -- but the shift units are in pixels/voxels, so you=20=
> would have to resample the dataset first to achieve sub-voxel shift.
if you resample the data to smaller pixels you need to be very sure how =
that is done,=20
so that you dont destroy the intensity data in the image.=20
Intensities need to be kept nice, since that how the coloc methods asses =
goodness of signal overlap.=20
Perhaps Kevin can explain the maths behind how imaris resamples an image =
to smaller pixels.=20
I dont see a good explanation in the docs... maybe i missed it.=20
The only safe resample method is a whole pixel binning...=20
but that making the pixels bigger.=20
To make them smaller you need to interpolate somehow...
and the way you do that is critical for not destroying the image =
intensity data.=20
Kevin?
>=20
> If you had the ImarisTrack module (unfortunately looks like you =
don't),=20
> there is also a "Drift Correction" function that could be applied with=20=
> sub-voxel precision automatically (first would need to swap the time &=20=
> channel axes, then correct drift, then swap them back again).=20
Again an explanation of how that really does the maths would be really =
great,=20
especially since one must have no black boxes.=20
or else one can not publish honestly.=20
Where do i find a mathematical explanation of how this sub pixel image =
shifting is done,=20
and how can i be sure image intensities are not destroyed do to a bad =
interpolation method?
Is it in the docs?
cheers
Dan
>=20
> Best regards,
> -Kevin
>=20
> Kevin Frischmann
> Head of Technical Support, US & Canada
> Bitplane, Inc.
> tel: +1 888-332-4879, ext. 11
> fax: 866-691-9112
>
[hidden email]
Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities=20
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany
+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)
http://www.bioimagexd.net BioImageXD
http://pacific.mpi-cbg.de Fiji - is just ImageJ =
(Batteries Included)
http://www.chalkie.org.uk Dan's Homepages
https://ifn.mpi-cbg.de Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )
------------------------------
Date: Wed, 26 May 2010 11:23:56 +0200
From: Juan Luis Ribas <
[hidden email]>
Subject: Primary dochroics in A1r
Dear list,
Does anyone have access to the transmision curves from the low-angle
incidence dichroic mirrors installed in the Nikon A1r?
Best regards
Juan Luis
--
Juan Luis Ribas
Servicio de MicroscopÃa
Centro de Investigación, TecnologÃa e Innovación
Universidad de Sevilla
Av. Reina Mercedes 4b
41012 Sevilla
Tfno: 954559983
------------------------------
Date: Wed, 26 May 2010 20:35:07 +0530
From: Roshma Azeem <
[hidden email]>
Subject: Re: Resonant scanner from A1R vs SP5 ...
--0016369207427c784004878099f8
Content-Type: text/plain; charset=ISO-8859-1
Hi Mac,
Fast acquisition time is required to analyze rapid biological processes in a
cell. Resonant scanners are about 10 times faster compared to the speed of
conventional scanners that are able to acquire fast frame recording and
provide real time live images. Due to the faster frame rate, they are useful
in resolving the complicated dynamic changes in living cells.
Resonant scanners have some disadvantages like higher readout noise. In
addition, their duty cycle is short as resonant scanners accelerate fast
that may affect the scanning mirror .
Further technical information can be seen at the following sites:
http://www.microscopyu.com/tutorials/flash/resonantscanning/confocalresonantscanning/index.htmlhttp://www.microscopyu.com/articles/confocal/resonantscanning.htmlNikon's A1R has a hybrid scanner and the SP5 has tandem scanner.
Roshma.
--0016369207427c784004878099f8
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
<br>Hi Mac, <br><br>Fast acquisition time is required to analyze rapid biol=
ogical=20
processes in a cell. Resonant scanners are about 10 times faster compared t=
o the speed of conventional scanners that are able to acquire fast frame re=
cording and provide real time live images. Due to the faster frame rate, th=
ey are useful in resolving the complicated dynamic changes in=20
living cells.<br><br>Resonant scanners have some disadvantages like higher =
readout noise. In addition, their duty cycle is short as resonant scanners =
accelerate fast that may affect the scanning mirror .<br><br>Further techni=
cal information can be seen at the following sites: <br>
<br><a href=3D"
http://www.microscopyu.com/tutorials/flash/resonantscanning/=confocalresonantscanning/index.html">
http://www.microscopyu.com/tutorials/f=lash/resonantscanning/confocalresonantscanning/index.html</a><br><br><a hre=
f=3D"
http://www.microscopyu.com/articles/confocal/resonantscanning.html">ht=
tp://www.microscopyu.com/articles/confocal/resonantscanning.html</a><br>
<br><br>Nikon's A1R has a hybrid scanner and the SP5 has tandem scanner=
. <br><br><br>Roshma.<br>
--0016369207427c784004878099f8--
------------------------------
Date: Thu, 27 May 2010 04:00:28 +1000
From: Mark Dupal <
[hidden email]>
Subject: AUTO: Dupal, Mark is out of the office. (returning 28/05/2010)
I am out of the office until 28/05/2010.
I will have limited email access and will respond to your message when I
return.
Note: This is an automated response to your message "Re: Resonant scanner
from A1R vs SP5 ..." sent on 5/27/2010 1:05:07 AM.
This is the only notification you will receive while this person is away.
P Please consider the environment before printing this email - 3 sheets o=
f A4 paper =3D 1 litre of water This message is intended only for the addre=
ssee. If you are not the intended recipient you are notified that disclos=
ing, copying, distributing or taking any action in reliance of the contents=
of this information is strictly prohibited. =
------------------------------
Date: Wed, 26 May 2010 11:32:12 -0700
From: Bob Nienhuis <
[hidden email]>
Subject: Poor man's confocal
--0016362837d817d8ce0487837ecd
Content-Type: text/plain; charset=ISO-8859-1
Anybody have any experience with the Zeiss Apotome structured illumination
system?
I am writing a proposal for a new microscope system and the vendor mentioned
this as a way
to reduce background in fluorescence microscopy.
Apparently, it superimposes a moving grid on the image, and this somehow
allows background
noise reduction.
We have used deconvolution to do this, but find that it takes a long time to
do.
I think it would add about $20k to the cost of the scope.
Opinions? Worthwhile? Any experience with it?
Bob Nienhuis
Neurobiology Research M/S151A3
UCLA / VA Medical Center
North Hills, CA
[hidden email]
--0016362837d817d8ce0487837ecd
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
<div>Anybody have any experience with the Zeiss Apotome structured illumina=
tion system?</div>
<div>=A0</div>
<div>I am writing a proposal for a new microscope system and the vendor men=
tioned this as a way</div>
<div>to reduce background in fluorescence microscopy.</div>
<div>=A0</div>
<div>Apparently, it superimposes a moving grid on the image, and this someh=
ow allows background</div>
<div>noise reduction. </div>
<div>=A0</div>
<div>We have used deconvolution to do this, but find that it takes a long t=
ime to do.</div>
<div>=A0</div>
<div>I think it would add about $20k to the cost of the scope.</div>
<div>=A0</div>
<div>Opinions? Worthwhile? Any experience with it?</div>
<div>=A0</div>
<div>Bob Nienhuis</div>
<div>Neurobiology Research M/S151A3</div>
<div>UCLA / VA Medical Center</div>
<div>North Hills, CA </div>
<div><a href=3D"mailto:
[hidden email]">
[hidden email]</a></=
div>
--0016362837d817d8ce0487837ecd--
------------------------------
Date: Wed, 26 May 2010 14:44:53 -0400
From: Joel Sheffield <
[hidden email]>
Subject: Re: Poor man's confocal
There has been a great deal of discusion of structured illumination
recently. You might take a look at NATUREMETHODS VOL.6NO.5:339
for one example. In addition to the Apotome modification, there is
also an add-on for other microscopes by Optigrid.
(
http://www.qioptiqlinos.com/Products/StructuredLightSystem/)
I haven't used either system, but I am also interested. Let me know
what you find out.
Joel
-------------- Original message ---------------
Anybody have any experience with the Zeiss Apotome structured
illumination system?
I am writing a proposal for a new microscope system and the vendor
mentioned this as a way
to reduce background in fluorescence microscopy.
Apparently, it superimposes a moving grid on the image, and this
somehow allows background
noise reduction.
We have used deconvolution to do this, but find that it takes a long
time to do.
I think it would add about $20k to the cost of the scope.
Opinions? Worthwhile? Any experience with it?
Bob Nienhuis
Neurobiology Research M/S151A3
UCLA / VA Medical Center
North Hills, CA
[hidden email]
--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]
(215) 204 8839, fax (215) 204 0486
http://astro.temple.edu/~jbs------------------------------
Date: Wed, 26 May 2010 15:52:27 -0400
From: Dale Callaham <
[hidden email]>
Subject: Re: Poor man's confocal
I have just finished training a user who came to us because the Apotome
system did not give anything like the results of the LSM510. I certainly
don't mean to suggest the Apotome system doesn't work, but you should
get a demo on your samples to see how it works for you.
Dale
Joel Sheffield wrote:
> There has been a great deal of discusion of structured illumination
> recently. You might take a look at NATUREMETHODS VOL.6NO.5:339
> for one example. In addition to the Apotome modification, there is
> also an add-on for other microscopes by Optigrid.
> (
http://www.qioptiqlinos.com/Products/StructuredLightSystem/)
>
> I haven't used either system, but I am also interested. Let me know
> what you find out.
>
> Joel
>
> -------------- Original message ---------------
> Anybody have any experience with the Zeiss Apotome structured
> illumination system?
>
> I am writing a proposal for a new microscope system and the vendor
> mentioned this as a way
> to reduce background in fluorescence microscopy.
>
> Apparently, it superimposes a moving grid on the image, and this
> somehow allows background
> noise reduction.
>
> We have used deconvolution to do this, but find that it takes a long
> time to do.
>
> I think it would add about $20k to the cost of the scope.
>
> Opinions? Worthwhile? Any experience with it?
>
> Bob Nienhuis
> Neurobiology Research M/S151A3
> UCLA / VA Medical Center
> North Hills, CA
>
[hidden email]
> --
> Joel B. Sheffield, Ph.D.
> Biology Department, Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
>
[hidden email]
> (215) 204 8839, fax (215) 204 0486
>
http://astro.temple.edu/~jbs------------------------------
Date: Wed, 26 May 2010 15:00:05 -0500
From: "Vergara, Leoncio A." <
[hidden email]>
Subject: Re: Poor man's confocal
I been told the images of the apotome are not quantitative... If that is t=
rue, that seems to me a big limitation of using the apotome for any serious=
fluorescence microscopy application.=20
Leoncio=20
-----Original Message-----
From: Confocal Microscopy List [mailto:
[hidden email]] On=
Behalf Of Dale Callaham
Sent: Wednesday, May 26, 2010 2:52 PM
To:
[hidden email]
Subject: Re: Poor man's confocal
I have just finished training a user who came to us because the Apotome sys=
tem did not give anything like the results of the LSM510. I certainly don't=
mean to suggest the Apotome system doesn't work, but you should get a demo=
on your samples to see how it works for you.
Dale
Joel Sheffield wrote:
> There has been a great deal of discusion of structured illumination=20
> recently. You might take a look at NATUREMETHODS VOL.6NO.5:339 for=20
> one example. In addition to the Apotome modification, there is also=20
> an add-on for other microscopes by Optigrid.
> (
http://www.qioptiqlinos.com/Products/StructuredLightSystem/)
>
> I haven't used either system, but I am also interested. Let me know=20
> what you find out.
>
> Joel
>
> -------------- Original message --------------- Anybody have any=20
> experience with the Zeiss Apotome structured illumination system?
>
> I am writing a proposal for a new microscope system and the vendor=20
> mentioned this as a way to reduce background in fluorescence=20
> microscopy.
>
> Apparently, it superimposes a moving grid on the image, and this=20
> somehow allows background noise reduction.
>
> We have used deconvolution to do this, but find that it takes a long=20
> time to do.
>
> I think it would add about $20k to the cost of the scope.
>
> Opinions? Worthwhile? Any experience with it?
>
> Bob Nienhuis
> Neurobiology Research M/S151A3
> UCLA / VA Medical Center
> North Hills, CA
>
[hidden email]
> --
> Joel B. Sheffield, Ph.D.
> Biology Department, Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
>
[hidden email]
> (215) 204 8839, fax (215) 204 0486
>
http://astro.temple.edu/~jbs------------------------------
Date: Thu, 27 May 2010 09:35:43 +0530
From: Roshma Azeem <
[hidden email]>
Subject: Re: Poor man's confocal
--001636e0a6c4223f7c04878b813a
Content-Type: text/plain; charset=ISO-8859-1
Hi Bob,
The performance of a structured illumination system may be close to the
capabilities of a confocal microscope but this cannot be an alternative for
CLSM. The performance difference is considerably high and Apotome has no
flexibility like confocal. This can be used as entry level optical
sectioning equipment.
In my opinion, this can be used as a pre-scanning system before we do
specimen analysis with CLSM. We can filter the number of specimen to be
analyzed with CLSM.
If I am not mistaken, Apotome cannot be fitted with any other microscope as
it is designed for Zeiss systems. However, OptiGrid can be fitted with any
existing microscopes. In addition, the buyer can select the CCD/EMCCD of
their choice.
Why not consider going for an entry level CLSM like Nikon C1 plus or Olympus
FV10i that may cost less than or almost the same cost of Apotome +
Microscope, but you get the real uncompromising result of confocal
microscopy?
Roshma.
On Thu, May 27, 2010 at 12:02 AM, Bob Nienhuis <
[hidden email]>wrote:
> Anybody have any experience with the Zeiss Apotome structured illumination
> system?
>
> I am writing a proposal for a new microscope system and the vendor
> mentioned this as a way
> to reduce background in fluorescence microscopy.
>
> Apparently, it superimposes a moving grid on the image, and this somehow
> allows background
> noise reduction.
>
> We have used deconvolution to do this, but find that it takes a long time
> to do.
>
> I think it would add about $20k to the cost of the scope.
>
> Opinions? Worthwhile? Any experience with it?
>
> Bob Nienhuis
> Neurobiology Research M/S151A3
> UCLA / VA Medical Center
> North Hills, CA
>
[hidden email]
>
--001636e0a6c4223f7c04878b813a
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
<br>Hi Bob,<br><br>The performance of a structured illumination system may =
be close to the capabilities of a confocal microscope but this cannot be an=
alternative for CLSM. The performance difference is considerably high and =
Apotome has no flexibility like confocal. This can be used as entry level o=
ptical sectioning equipment. <br>
<br>In my opinion, this can be used as a pre-scanning system before we do s=
pecimen analysis with CLSM. We can filter the number of specimen to be anal=
yzed with CLSM. <br><br>If I am not mistaken, Apotome cannot be fitted with=
any other microscope as it is designed for Zeiss systems. However, OptiGri=
d can be fitted with any existing microscopes. In addition, the buyer can s=
elect the CCD/EMCCD of their choice.<br>
<br>Why not consider going for an entry level CLSM like Nikon C1 plus or Ol=
ympus FV10i that may cost less than or almost the same cost of Apotome + Mi=
croscope, but you get the real uncompromising result of confocal microscopy=
?<br>
<br>Roshma.<br><br><br><br><div class=3D"gmail_quote">On Thu, May 27, 2010 =
at 12:02 AM, Bob Nienhuis <span dir=3D"ltr"><<a href=3D"mailto:bob.nienh=
[hidden email]">
[hidden email]</a>></span> wrote:<br><blockquote =
class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; border-left: 1px =
solid rgb(204, 204, 204); padding-left: 1ex;">
<div>Anybody have any experience with the Zeiss Apotome structured illumina=
tion system?</div>
<div>=A0</div>
<div>I am writing a proposal for a new microscope system and the vendor men=
tioned this as a way</div>
<div>to reduce background in fluorescence microscopy.</div>
<div>=A0</div>
<div>Apparently, it superimposes a moving grid on the image, and this someh=
ow allows background</div>
<div>noise reduction. </div>
<div>=A0</div>
<div>We have used deconvolution to do this, but find that it takes a long t=
ime to do.</div>
<div>=A0</div>
<div>I think it would add about $20k to the cost of the scope.</div>
<div>=A0</div>
<div>Opinions? Worthwhile? Any experience with it?</div>
<div>=A0</div>
<div>Bob Nienhuis</div>
<div>Neurobiology Research M/S151A3</div>
<div>UCLA / VA Medical Center</div>
<div>North Hills, CA </div>
<div><a href=3D"mailto:
[hidden email]" target=3D"_blank">Bob.Nienhu=
[hidden email]</a></div>
</blockquote></div><br>
--001636e0a6c4223f7c04878b813a--
------------------------------
End of CONFOCALMICROSCOPY Digest - 25 May 2010 to 26 May 2010 (#2010-16)
************************************************************************