http://confocal-microscopy-list.275.s1.nabble.com/Re-CONFOCALMICROSCOPY-Digest-25-May-2010-to-26-May-2010-2010-16-tp5107012p5107819.html
> 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: 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)
>> ************************************************************************
>