http://confocal-microscopy-list.275.s1.nabble.com/Re-CONFOCALMICROSCOPY-Digest-25-May-2010-to-26-May-2010-2010-16-tp5107012p5107773.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 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'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)
> ************************************************************************