Re: CONFOCALMICROSCOPY Digest - 25 May 2010 to 26 May 2010 (#2010-16)

[Jason Brenner]

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: [phone]
[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: [phone], ext. 11
> fax: [phone]
> [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

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (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 Microscopía
Centro de Investigación, Tecnología 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.html

http://www.microscopyu.com/articles/confocal/resonantscanning.html


Nikon'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&#39;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]
[phone], fax [phone]
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]
> [phone], fax [phone]
> 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]
> [phone], fax [phone]
> 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">&lt;<a href=3D"mailto:bob.nienh=
[hidden email]">[hidden email]</a>&gt;</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)
************************************************************************

[Peter Gabriel Pitrone]

Jason,

I love you too...

Smooches,

On May 27, 2010, at 07:10 AM, [hidden email] wrote:

> 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: [phone]
> [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: [phone], ext. 11
>> fax: [phone]
>> [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
>
> [phone] (German Mobile)
> [phone] (Work phone at MPI-CBG)
> [phone] (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 Microscopía
> Centro de Investigación, Tecnología 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.html
>
> http://www.microscopyu.com/articles/confocal/resonantscanning.html
>
>
> Nikon'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&#39;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]
> [phone], fax [phone]
> 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]
>> [phone], fax [phone]
>> 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]
>> [phone], fax [phone]
>> 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">&lt;<a href=3D"mailto:bob.nienh=
> [hidden email]">[hidden email]</a>&gt;</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)
> ************************************************************************

[lechristophe]

Lots of love for you all !

Christophe

On Thu, May 27, 2010 at 11:38, Peter Pitrone <[hidden email]> wrote:

> Jason,
>
> I love you too...
>
> Smooches,
>
> On May 27, 2010, at 07:10 AM, [hidden email] wrote:
>
>> 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: [phone]
>> [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: [phone], ext. 11
>>> fax: [phone]
>>> [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
>>
>> [phone] (German Mobile)
>> [phone] (Work phone at MPI-CBG)
>> [phone] (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 Microscopía
>> Centro de Investigación, Tecnología 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.html
>>
>> http://www.microscopyu.com/articles/confocal/resonantscanning.html
>>
>>
>> Nikon'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&#39;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]
>> [phone], fax [phone]
>> 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]
>>> [phone], fax [phone]
>>> 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]
>>> [phone], fax [phone]
>>> 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">&lt;<a href=3D"mailto:bob.nienh=
>> [hidden email]">[hidden email]</a>&gt;</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)
>> ************************************************************************
>

[Eric Scarfone]

I "love" this thread!
Eric

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: [phone],
Cell: [phone]
Fax: [phone]

email: [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Christophe Leterrier <[hidden email]>
Date: Thursday, May 27, 2010 11:58 am
Subject: Re: CONFOCALMICROSCOPY Digest - 25 May 2010 to 26 May 2010 (#2010-16)
To: [hidden email]

> Lots of love for you all !
>
> Christophe
>
> On Thu, May 27, 2010 at 11:38, Peter Pitrone <[hidden email]>
> wrote:> Jason,
> >
> > I love you too...
> >
> > Smooches,
> >

> > On May 27, 2010, at 07:10 AM, [hidden email] wrote:

> >
> >> 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: [phone]
> >> [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: [phone], ext. 11
> >>> fax: [phone]
> >>> [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
> >>
> >> [phone] (German Mobile)
> >> [phone] (Work phone at MPI-CBG)
> >> [phone] (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 Microscopía
> >> Centro de Investigación, Tecnología 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.html>>
> >> http://www.microscopyu.com/articles/confocal/resonantscanning.html
> >>
> >>
> >> Nikon'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>http://www.microscopyu.com/tutorials/flash/resonantscanning/=

> >>
> confocalresonantscanning/index.html">http://www.microscopyu.com/tutorials/f=>> lash/resonantscanning/confocalresonantscanning/index.html<br><br>>> f=3D"http://www.microscopyu.com/articles/confocal/resonantscanning.html">ht=
> >>
> tp://www.microscopyu.com/articles/confocal/resonantscanning.html<br>>> <br><br>Nikon&#39;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>mailto:[hidden email]">[hidden email]</=
> >> 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]
> >> [phone], fax [phone]
> >> 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]
> >>> [phone], fax [phone]
> >>> 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]
> >>> [phone], fax [phone]
> >>> 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"><mailto:bob.nienh=
> >> [hidden email]">[hidden email]&gt;</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>mailto:[hidden email]" target=3D"_blank">Bob.Nienhu=
> >> [hidden email]</div>
> >> </blockquote></div><br>
> >>
> >> --001636e0a6c4223f7c04878b813a--
> >>
> >> ------------------------------
> >>
> >> End of CONFOCALMICROSCOPY Digest - 25 May 2010 to 26 May 2010
> (#2010-16)
> >>
> ************************************************************************>
>

[Straatman, Kees (Dr.)]

Dear list members,

From 23-27 August 2010 I organize, in collaboration with commercial partners, two workshops at the university of Leicester, UK. The first day is an immunolabelling workshop followed by a 4 day fluorescence microscopy workshop under the combined title: 'From basic to advanced microscopy'. The workshops include lectures and hands-on sessions/demonstrations. For further information, program and application form please visit: http://www.le.ac.uk/biochem/microscopy/workshop2010.html.

Confirmed equipment available during the workshop:

- Olympus FV1000 confocal laser scanning microscope
- Olympus cell^R imaging analysis
- Nikon Eclipse Ti-E microscope with A1R Confocal
- Leica TCS SP5 confocal laser scanning microscope
- Zeiss LSM7 multiphoton laser scanning microscope
- LIFA, Lambert Instruments Fluorescence Attachment for FLIM
- PerkinElmer UltraVIEW VoX spinning disk confocal microscope
- Improvision's high performance 3D imaging software package Volocity
- Imaris, the cutting-Edge 3D and 4D Imaging Software for Life Sciences from Bitplane
- Huygens deconvolution software from SVI


Best wishes

Kees


Dr K.R. Straatman
Senior Experimental Officer
College of Medicine, Biological Sciences and Psychology
http://www.le.ac.uk/biochem/microscopy/home.html

Postal address:
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Rd.
Leicester LE1 9HN
UK
tel.: + 44 (0)116 229 7085/252 2263
fax: + 44 (0)116 229 7031

Times Higher Education Award for Outstanding Student Support 2009-10

Times Higher Education University of the Year 2008-9

[Alberto Diaspro]

Dear friends
we have seats available for the following Microscopy events:

3 seats - free of charge
Director: A.Diaspro
Practical School of Confocal/Multiphoton/Superesolution School at the Italian Institute of Technology - Genoa, Italy. (www.iit.it)
info: [hidden email] or [hidden email]


8 seats - 900 Euros including lodging and meals (plus large screen for the Footbal Worldchampionship final, upon the arrival on July 11th)
Directors: G.J. Brakenhoff, A.Diaspro
Italian Physical Society International Course at the "Enrico Fermi" School, Advanced methods in Optical Fluorescence MIcroscopy towards Nnaoscopy. !2-17 July, Varenna, Como Lake, Italy. (www.sif.it)
info: [hidden email] or [hidden email]


See you in Italy this Summer.
Ciao
Alby

[Anchal Chandra]

Hello,

I am interested in applying for this course.How can I apply for these seats.The application deadline is already over.Can I still apply.

Kindly reply

On Thu, May 27, 2010 at 3:47 PM, Alberto Diaspro <[hidden email]> wrote:

Dear friends
we have seats available for the following Microscopy events:

3 seats - free of charge
Director: A.Diaspro
Practical School of Confocal/Multiphoton/Superesolution School at the Italian Institute of Technology - Genoa, Italy. (www.iit.it)
info: [hidden email] or [hidden email]


8 seats - 900 Euros including lodging and meals (plus large screen for the Footbal Worldchampionship final, upon the arrival on July 11th)
Directors: G.J. Brakenhoff, A.Diaspro
Italian Physical Society International Course at the "Enrico Fermi" School, Advanced methods in Optical Fluorescence MIcroscopy towards Nnaoscopy. !2-17 July, Varenna, Como Lake, Italy. (www.sif.it)
info: [hidden email] or [hidden email]


See you in Italy this Summer.
Ciao
Alby

[Dan Focht]

Bio-imagers


Over the years there have been many postings about glass bottomed dishes.
At the time of these post Bioptechs was not in a position to release a product of the type described herein.
We have completed development and manufacture of a product that I believe you will find both economical and useful.

Introducing the ICD Interchangeable Coverslip Dish.  

Features:
Only replace the coverslip after use
No metal comes in contact with cells or media
German #1.5 30mm coverslip w/25mm viewing aperture
Autoclaveable
Fits in any 35mm warmer
O-ring seal assures no leakage

Further details available at:

http://www.bioptechs.com/Products/ICD/coverslipdish.html


I hope you find this announcement useful.  
Bioptechs is a private company that grew out of academic research and uses no public funds to develop or manufacture its products.
If you find this message offensive send all admonishments to: [hidden email]



Dan


Dan Focht
Bioptechs, Inc.
3560 Beck Rd.
Butler, PA 16002
www.bioptechs.com
P: [phone]
F: [phone]
[hidden email]

[Straatman, Kees (Dr.)]

Dear list members,

There are still places available for the fluorescence microscopy workshops at the University of Leicester, UK, from 23 - 27 August 2010.

The first day is an immunolabelling workshop followed by a 4 days fluorescence microscopy workshop under the combined title: 'From basic to advanced microscopy'. The workshops include lectures and hands-on sessions/demonstrations. For further information, program and application form please visit: http://www.le.ac.uk/biochem/microscopy/workshop2010.html.
 
Equipment available during the workshop:

- Olympus FV1000 confocal laser scanning microscope
- Olympus cell^R imaging analysis
- Nikon A1R confocal laser scanning microscope
- Leica TCS SP5 confocal laser scanning microscope
- Zeiss LSM7 multiphoton laser scanning microscope
- FLIM, Lambert Instruments
- PerkinElmer UltraVIEW VoX spinning disk confocal microscope
- Imprecision's high performance 3D imaging software package Volocity
- Imaris, the cutting-Edge 3D and 4D Imaging Software for Life Sciences from Bitplane


Best wishes

Kees


Dr K.R. Straatman
Senior Experimental Officer
College of Medicine, Biological Sciences and Psychology
http://www.le.ac.uk/biochem/microscopy/home.html

Postal address:
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Rd.
Leicester LE1 9HN
UK
tel.: + 44 (0)116 229 7085/252 2263
fax: + 44 (0)116 229 7031

Times Higher Education Award for Outstanding Student Support 2009-10

Times Higher Education University of the Year 2008-9