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Dear All,
Does anyone has recommendations on from where to by a transparent Richardson test slide for phase imaging? I have found couple of companies with google and also some pages of researchers that suggest that very few companies provide well calibrated slides. The original manufacturer's website: www.richardson-tech.com is down. Thanks in advance for inputs shalin -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm |
Barbara Foster |
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Hi, Shalin
Unfortunately, Richardson has gone out of business. You might try EMS Diatome. They were one of Richardson's strongest supporters. Good hunting, Barbara At 04:50 PM 6/18/2008, you wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All, |
Shalin Mehta |
Search the CONFOCAL archive at
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Thanks Barbara,
EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email. Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells. btw folks, pardon the 'blurred' English in last mail. cheers Shalin On Thu, Jun 19, 2008 at 9:23 PM, Barbara Foster <[hidden email]> wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm |
Sam's Mail |
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Why not use the everpresent molecular probes test slides? FluoCells prepared slide #3 would be a likely candidate. I use it for fluorescent and DIC alignment checks often. It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs. Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too. -- Samuel A. Connell Director of Light Microscopy Cell & Tissue Imaging Center St. Jude Children's Research Hospital 332 North Lauderdale St., E7061 Memphis, TN 38105-2794 (901) 495-2536 [hidden email] ________________________________________ From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]] Sent: Thursday, June 19, 2008 7:47 PM To: [hidden email] Subject: Re: Source of Richardson test slide. . Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara, EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email. Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells. btw folks, pardon the 'blurred' English in last mail. cheers Shalin On Thu, Jun 19, 2008 at 9:23 PM, Barbara Foster <[hidden email]<mailto:[hidden email]>> wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi, Shalin Unfortunately, Richardson has gone out of business. You might try EMS Diatome. They were one of Richardson's strongest supporters. Good hunting, Barbara At 04:50 PM 6/18/2008, you wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All, Does anyone has recommendations on from where to by a transparent Richardson test slide for phase imaging? I have found couple of companies with google and also some pages of researchers that suggest that very few companies provide well calibrated slides. The original manufacturer's website: www.richardson-tech.com<http://www.richardson-tech.com> is down. Thanks in advance for inputs shalin -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com<http://shalin.wordpress.com> ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com<http://shalin.wordpress.com> ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm |
Shalin Mehta |
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I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf
We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells. cheers shalin On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote: Search the CONFOCAL archive at |
James Pawley |
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Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf Roger Tsien used to recommend putting diatom frustules into
immersion oil with dye in it.
Jim P.
On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote: --
****************************************
Prof. James B. Pawley, Phone: 604-822-7801 3D Microscopy of Living Cells: Summer Course CELL: 778-861-2874 "If it isn't diffraction, it is statistics":Microscopist's complaint, Anon. |
Eric Scarfone |
In reply to this post by Shalin Mehta
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Reading Shalin Mehta abstract I am not sure I understand how assymetric illumination is achieved? I this is equivalent to the technique used in video microscopy (ie: Kachar B. Asymmetric illumination contrast: a method of image formation for video light microscopy. Science. 1985 Feb 15;227(4688):766-8) shouldn't you put half aperture stops at the back focal plane of the obejective and not of the condenser? Or did I get it wrong? 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: +46 (0)8-517 79343, Cell: +46 (0)70 888 2352 Fax: +46 (0)8-301876 email: [hidden email] http://www.ki.se/cfh/ ----- Original Message ----- From: Shalin Mehta <[hidden email]> Date: Saturday, June 21, 2008 4:25 am Subject: Re: Source of Richardson test slide. . To: [hidden email] > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > I should have clarified. I am working on a method for imaging cell > cultureson plastic in bas-relief. At the risk of self-promotion, I > am posting link > to the recent conference presentation: > http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf > > We think it will be useful for quantitative (or atleast semi- > quantitative)measurements of optical thickness. So I am looking > for some well > characterized test specimen (whose hight profile is known) which > resembleoptical thickness of cells. > > cheers > shalin > > > > On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel > <[hidden email]>wrote: > > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > > > Why not use the everpresent molecular probes test slides? > > prepared slide #3 would be a likely candidate. I use it for > fluorescent and > > DIC alignment checks often. It's 16um thick, so perhaps for an > unknown> reason to me, that might not meet your needs. Some of > the other FluoCells > > prepared slides are cultured cells rather than sections, so you > might like > > them too. > > -- > > Samuel A. Connell > > Director of Light Microscopy > > Cell & Tissue Imaging Center > > St. Jude Children's Research Hospital > > 332 North Lauderdale St., E7061 > > Memphis, TN 38105-2794 > > (901) 495-2536 > > [hidden email] > > > > > > ________________________________________ > > From: Confocal Microscopy List [[hidden email]] > On Behalf > > Of Shalin Mehta [[hidden email]] > > Sent: Thursday, June 19, 2008 7:47 PM > > To: [hidden email] > > Subject: Re: Source of Richardson test slide. . > > > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks > Barbara,> EMS doesn't list the Richardson slide on website any > more. I am waiting > > for the reply to email. > > Is there any other known phase contrast test specimen? One could > > diatoms but they are rather 'active' optically. I would like > something that > > resembles (within a factor of 2 or 3) optical thickness of cells. > > btw folks, pardon the 'blurred' English in last mail. > > > > cheers > > Shalin > > > |
Shalin Mehta |
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Hi Eric,
You are almost correct. Yes it is equivalent to Kachar's asymmetric illumination. Only reason Kachar is not mentioned in the abstract is lack of space, in my actual presentation I had motivated the phase gradient contrast without use of interference (as in DIC) from his paper. Kachar had also used asymmetric illumination on condenser side. If you look at his Figure 2, he has offset the filament such that only one half of the condenser fills the BFP of condenser. Quating verbatim from his paper: "To obtain asymmetric illumination, the lamp filament is simply displaced from the optical axis (Fig. 2a). With the filament offset, the regular diffuser glass in front of the lamp spreads the light to fill the condenser aperture with a gradi- ent of illumination (Fig. 2b). This gradi- ent provides the requisite imbalance of oblique rays. " But you are right that putting a block in objective BFP will also produce phase gradient contrast (as is done by some researchers early and recently: Axelrod - "Zero cost modification for phase imaging" or similar title Jerome Mertz group - "Graded field microscopy white light microscopy" ) Of course, the problem with objective side block is that you lose NA. However, if that is the only thing accessible and one wants just phase gradient contrast, it is perfectly OK. The difference is AI-DPC (as we like to call our method) is more quantitative in nature and separates phase information (optical thickness) and amplitude information (light absorbption) that you can super-impose later if you like. We are in process of writing up the thing and if you like further details about quantitative nature we could discuss off-list. We will also be very glad to see if some of you try this and have good/bad things to say about it. Cheers shalin On Sat, Jun 21, 2008 at 11:26 PM, Eric Scarfone <[hidden email]> wrote: Search the CONFOCAL archive at -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm |
Shalin Mehta |
In reply to this post by Shalin Mehta
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Hello Jim,
Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use? Cheers Shalin On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote:
-- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm |
Search the CONFOCAL archive at
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I think the idea is that the dye will be a 'negative
stain'. But I have to
say that I don't think diatoms will be useful for your
purpose since
the phase differences in the thicker areas such as the
raphe are too
great and the structure in the thinner parts is too
complex.
Maybe one of the filter companies, who have the facilities
for precise
deposition of layers of known refractive index, could
create a
patterned slide? Any comments from the
companies?
Guy
Optical Imaging Techniques in Cell Biology From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shalin Mehta Sent: Sunday, 22 June 2008 1:26 PM To: [hidden email] Subject: Re: Source of Richardson test slide. . Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use? Cheers Shalin On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote:
-- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm No virus found in this incoming message. No virus found in this outgoing message. |
Shalin Mehta |
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks for clarification Guy. 'negative stain' is new to me. I agree with you about diatom's complex structures - their periodic nature introduces diffraction effects of their own and I have seen differences in contrast seen with cells and diatoms. But in absence of other things, not bad to try. I found a diatom on net that seems smooth - but no idea where to get it or whether it has unresolved fine structure. I will be glad to see if some company is willing to prepare a slide as Guy suggests. I have an inkling that AFM community has some transparent patterned height standard to calibrate their equipment. I have seen a paper (Spiral phase contrast imaging in microscopy) where measurements of optical phase and AFM are compared. Still looking for it. Any word from AFM people? Is there an equivalent of confocal list for AFM that anyone knows of? People around me who do AFM haven't yet suggested transparent test slides. Cheers Shalin On Sun, Jun 22, 2008 at 12:08 PM, Guy Cox <[hidden email]> wrote: > > Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > I think the idea is that the dye will be a 'negative stain'. But I have to > say that I don't think diatoms will be useful for your purpose since > the phase differences in the thicker areas such as the raphe are too > great and the structure in the thinner parts is too complex. > > Maybe one of the filter companies, who have the facilities for precise > deposition of layers of known refractive index, could create a > patterned slide? Any comments from the companies? > > Guy > > > Optical Imaging Techniques in Cell Biology > by Guy Cox CRC Press / Taylor & Francis > http://www.guycox.com/optical.htm > ______________________________________________ > Associate Professor Guy Cox, MA, DPhil(Oxon) > Electron Microscope Unit, Madsen Building F09, > University of Sydney, NSW 2006 > ______________________________________________ > Phone +61 2 9351 3176 Fax +61 2 9351 7682 > Mobile 0413 281 861 > ______________________________________________ > http://www.guycox.net > > > ________________________________ > From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shalin Mehta > Sent: Sunday, 22 June 2008 1:26 PM > To: [hidden email] > Subject: Re: Source of Richardson test slide. . > > Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Jim, > > Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use? > > Cheers > Shalin > > On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote: >> >> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf >> >> We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells. >> >> cheers >> shalin >> >> >> Roger Tsien used to recommend putting diatom frustules into immersion oil with dye in it. >> Jim P. >> >> On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote: >> >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> Why not use the everpresent molecular probes test slides? FluoCells prepared slide #3 would be a likely candidate. I use it for fluorescent and DIC alignment checks often. It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs. Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too. >> -- >> Samuel A. Connell >> Director of Light Microscopy >> Cell & Tissue Imaging Center >> St. Jude Children's Research Hospital >> 332 North Lauderdale St., E7061 >> Memphis, TN 38105-2794 >> (901) 495-2536 >> [hidden email] >> >> >> ________________________________________ >> From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]] >> Sent: Thursday, June 19, 2008 7:47 PM >> To: [hidden email] >> Subject: Re: Source of Richardson test slide. . >> >> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara, >> EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email. >> Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells. >> btw folks, pardon the 'blurred' English in last mail. >> >> cheers >> Shalin >> >> -- >> >> **************************************** >> Prof. James B. Pawley, Phone: 604-822-7801 >> 3D Microscopy of Living Cells: Summer Course CELL: 778-861-2874 >> >> "If it isn't diffraction, it is statistics":Microscopist's complaint, Anon. > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~ > Shalin Mehta > mobile: +65-90694182 > blog: shalin.wordpress.com > ~~~~~~~~~~~~~~~~~~~~~~~~~~ > Bioimaging Lab, Block-E3A, #7-10 > Div of Bioengineering, NUS Singapore 117574 > website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html > > Liver Cancer Functional Genomics Lab, #6-05 > National Cancer Centre, Singapore 169610 > http://www.nccs.com.sg/researcher/02_04d.htm > > No virus found in this incoming message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM > > No virus found in this outgoing message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm |
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Negative staining simply means surrounding an unstained sample with a sea of stain. In principle this will just give a negative image compared to conventional staining. I used to have a glass slide with a known step in it but it was supplied as a calibration standard with a 'tally-step' (DekTak I think) so I don't know where you could buy one. That one got broken. But it would probably be worth checking the Agar Scientific catalogue - they're pretty good for such things. Guy Optical Imaging Techniques in Cell Biology by Guy Cox CRC Press / Taylor & Francis http://www.guycox.com/optical.htm ______________________________________________ Associate Professor Guy Cox, MA, DPhil(Oxon) Electron Microscope Unit, Madsen Building F09, University of Sydney, NSW 2006 ______________________________________________ Phone +61 2 9351 3176 Fax +61 2 9351 7682 Mobile 0413 281 861 ______________________________________________ http://www.guycox.net -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shalin Mehta Sent: Sunday, 22 June 2008 2:34 PM To: [hidden email] Subject: Re: Source of Richardson test slide. . Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks for clarification Guy. 'negative stain' is new to me. I agree with you about diatom's complex structures - their periodic nature introduces diffraction effects of their own and I have seen differences in contrast seen with cells and diatoms. But in absence of other things, not bad to try. I found a diatom on net that seems smooth - but no idea where to get it or whether it has unresolved fine structure. I will be glad to see if some company is willing to prepare a slide as Guy suggests. I have an inkling that AFM community has some transparent patterned height standard to calibrate their equipment. I have seen a paper (Spiral phase contrast imaging in microscopy) where measurements of optical phase and AFM are compared. Still looking for it. Any word from AFM people? Is there an equivalent of confocal list for AFM that anyone knows of? People around me who do AFM haven't yet suggested transparent test slides. Cheers Shalin On Sun, Jun 22, 2008 at 12:08 PM, Guy Cox <[hidden email]> wrote: > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > I think the idea is that the dye will be a 'negative stain'. But I > have to say that I don't think diatoms will be useful for your purpose > since the phase differences in the thicker areas such as the raphe are > too great and the structure in the thinner parts is too complex. > > Maybe one of the filter companies, who have the facilities for precise > deposition of layers of known refractive index, could create a > patterned slide? Any comments from the companies? > > > Guy > > > Optical Imaging Techniques in Cell Biology > by Guy Cox CRC Press / Taylor & Francis > http://www.guycox.com/optical.htm > ______________________________________________ > Associate Professor Guy Cox, MA, DPhil(Oxon) Electron Microscope Unit, > Madsen Building F09, University of Sydney, NSW 2006 > ______________________________________________ > Phone +61 2 9351 3176 Fax +61 2 9351 7682 > Mobile 0413 281 861 > ______________________________________________ > http://www.guycox.net > > > ________________________________ > From: Confocal Microscopy List [mailto:[hidden email]] > On Behalf Of Shalin Mehta > Sent: Sunday, 22 June 2008 1:26 PM > To: [hidden email] > Subject: Re: Source of Richardson test slide. . > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Jim, > > Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use? > > Cheers > Shalin > > On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote: >> >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have >> clarified. I am working on a method for imaging cell cultures on >> plastic in bas-relief. At the risk of self-promotion, I am posting >> link to the recent conference presentation: >> http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf >> >> We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells. >> >> cheers >> shalin >> >> >> Roger Tsien used to recommend putting diatom frustules into immersion oil with dye in it. >> Jim P. >> >> On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote: >> >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> Why not use the everpresent molecular probes test slides? FluoCells prepared slide #3 would be a likely candidate. I use it for fluorescent and DIC alignment checks often. It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs. Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too. >> -- >> Samuel A. Connell >> Director of Light Microscopy >> Cell & Tissue Imaging Center >> St. Jude Children's Research Hospital >> 332 North Lauderdale St., E7061 >> Memphis, TN 38105-2794 >> (901) 495-2536 >> [hidden email] >> >> >> ________________________________________ >> From: Confocal Microscopy List [[hidden email]] On >> Behalf Of Shalin Mehta [[hidden email]] >> Sent: Thursday, June 19, 2008 7:47 PM >> To: [hidden email] >> Subject: Re: Source of Richardson test slide. . >> >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara, EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email. >> Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells. >> btw folks, pardon the 'blurred' English in last mail. >> >> cheers >> Shalin >> >> -- >> >> **************************************** >> Prof. James B. Pawley, Phone: 604-822-7801 >> 3D Microscopy of Living Cells: Summer Course CELL: 778-861-2874 >> >> "If it isn't diffraction, it is statistics":Microscopist's complaint, Anon. > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~ > Shalin Mehta > mobile: +65-90694182 > blog: shalin.wordpress.com > ~~~~~~~~~~~~~~~~~~~~~~~~~~ > Bioimaging Lab, Block-E3A, #7-10 > Div of Bioengineering, NUS Singapore 117574 > website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html > > Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, > Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm > > No virus found in this incoming message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: > 21/06/2008 9:27 AM > > No virus found in this outgoing message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: > 21/06/2008 9:27 AM -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm No virus found in this incoming message. Checked by AVG. Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM No virus found in this outgoing message. Checked by AVG. Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM |
John Oreopoulos |
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I was a bit surprised at the statistics cited in this article: http://chronicle.com/free/2008/05/3028n.htm Does this mean that all journals will start hiring image manipulation detectives someday? Could be an interesting career. John Oreopoulos, BSc, PhD Candidate University of Toronto Institute For Biomaterials and Biomedical Engineering Centre For Studies in Molecular Imaging Tel: W:416-946-5022 |
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Interesting - especially the statement that images on film cannot be doctored. I guess it's irrelevant nowadays, but that is so far from the truth. One funny story - which I've told before but some time ago. Many years ago I (with colleagues) published a paper in a well-known journal which included a photo of some gels - taken by the departmental photographer. One of the gels had cracked when it was taken out of the tube, so there was a dark hairline across it in the photo. In the published paper that line had disappeared. You can hardly accuse me, or my two co-authors, of fraud since this was done by the journal's art department without any reference to us! Guy Optical Imaging Techniques in Cell Biology by Guy Cox CRC Press / Taylor & Francis http://www.guycox.com/optical.htm ______________________________________________ Associate Professor Guy Cox, MA, DPhil(Oxon) Electron Microscope Unit, Madsen Building F09, University of Sydney, NSW 2006 ______________________________________________ Phone +61 2 9351 3176 Fax +61 2 9351 7682 Mobile 0413 281 861 ______________________________________________ http://www.guycox.net -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos Sent: Sunday, 22 June 2008 10:57 PM To: [hidden email] Subject: An alarming amount of image manipulation Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I was a bit surprised at the statistics cited in this article: http://chronicle.com/free/2008/05/3028n.htm Does this mean that all journals will start hiring image manipulation detectives someday? Could be an interesting career. John Oreopoulos, BSc, PhD Candidate University of Toronto Institute For Biomaterials and Biomedical Engineering Centre For Studies in Molecular Imaging Tel: W:416-946-5022 No virus found in this incoming message. Checked by AVG. Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM No virus found in this outgoing message. Checked by AVG. Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM |
Shalin Mehta |
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal We realized it is a big concern these days when we took a course on ethics in research (mandatory for anyone doing bioengineering or life sciences here). We came across quite interesting cases of high profile fraud. We had to do a presentation and we presented something on image manipulation. While thinking about it I stumbled upon an interesting way of quickly checking fake data. It is to 'scan the histogram' with 'narrow look up table', i.e. set the contrast to maximum and view the image as you change the brightness. The idea being that when someone has merged different images to appear one or copied e.g. bands - scanning the histogram will show clear signs. In the case of merging,one can see an edge where merge has been done and in the case of copy one can see that two regions of the image change identically as we scan the histogram. With that, I found that I could actually detect discrepancies in example fake data given in Rossner's editorial (What is in a picture? by Rossner and Yamada). I tend to think that these problems will subside as ideas like open source, reproducible research (http://sepwww.stanford.edu/research/redoc/), and giving credit based on 'first appearance anywhere and not just journal' will permeate gradually - they have already done so in computer science where it is very easy to allow someone to reproduce your work simply by uploading files. cheers shalin On Sun, Jun 22, 2008 at 10:43 PM, Guy Cox <[hidden email]> wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Interesting - especially the statement that images on film > cannot be doctored. I guess it's irrelevant nowadays, but that > is so far from the truth. > > One funny story - which I've told before but some time ago. > Many years ago I (with colleagues) published a paper in a > well-known journal which included a photo of some gels - > taken by the departmental photographer. One of the gels had > cracked when it was taken out of the tube, so there was a > dark hairline across it in the photo. In the published paper > that line had disappeared. You can hardly accuse me, or my > two co-authors, of fraud since this was done by the journal's > art department without any reference to us! > > Guy > > > Optical Imaging Techniques in Cell Biology > by Guy Cox CRC Press / Taylor & Francis > http://www.guycox.com/optical.htm > ______________________________________________ > Associate Professor Guy Cox, MA, DPhil(Oxon) > Electron Microscope Unit, Madsen Building F09, > University of Sydney, NSW 2006 > ______________________________________________ > Phone +61 2 9351 3176 Fax +61 2 9351 7682 > Mobile 0413 281 861 > ______________________________________________ > http://www.guycox.net > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos > Sent: Sunday, 22 June 2008 10:57 PM > To: [hidden email] > Subject: An alarming amount of image manipulation > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > I was a bit surprised at the statistics cited in this article: > > http://chronicle.com/free/2008/05/3028n.htm > > Does this mean that all journals will start hiring image manipulation detectives someday? Could be an interesting career. > > > John Oreopoulos, BSc, > PhD Candidate > University of Toronto > Institute For Biomaterials and Biomedical Engineering Centre For Studies in Molecular Imaging > > Tel: W:416-946-5022 > > No virus found in this incoming message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM > > > No virus found in this outgoing message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM > > -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm |
Michael Cammer |
In reply to this post by Guy Cox
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal In my experience, when somebody shows up with micrographs that have cells pasted in or background "distractions" stamp tooled out and I suggest maybe taking more pictures or doing the experiment again, they complain that this would cost more and delay them. "The data are what they are and I'm just showing people and if I don't make it look good, then they won't publish it." Sometimes junior lab members will go back to their PIs and say that I wasn't helpful; I become the problem. I will not apologize for refusing to use the lasso tool around a band on a gel and S curve adjust it in Photoshop Curves or for refusing to paint out "an anomalous bad cell off in the corner of the image". Yes, both these requests have come through our facility along with a bunch of other egregious ones. Some scientists really feel justified because the competition does it. "Hey, everybody does it," they say. Although, more often (and a search will show that we've discussed this before), people simply don;t understand what they are doing. They simply misuse the tools for making figures. As with example of film, before you can begin to alter images in an intentional manner or make even reasonably good pictures of anything, you need to be at least knowledgeable of darkroom technique. But with the new digital tools, any dummy can be a photographer and can cut and paste and manipulate in complicated ways. -Michael > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Interesting - especially the statement that images on film > cannot be doctored. I guess it's irrelevant nowadays, but that > is so far from the truth. > > One funny story - which I've told before but some time ago. > Many years ago I (with colleagues) published a paper in a > well-known journal which included a photo of some gels - > taken by the departmental photographer. One of the gels had > cracked when it was taken out of the tube, so there was a > dark hairline across it in the photo. In the published paper > that line had disappeared. You can hardly accuse me, or my > two co-authors, of fraud since this was done by the journal's > art department without any reference to us! > > Guy > > > Optical Imaging Techniques in Cell Biology > by Guy Cox CRC Press / Taylor & Francis > http://www.guycox.com/optical.htm > ______________________________________________ > Associate Professor Guy Cox, MA, DPhil(Oxon) > Electron Microscope Unit, Madsen Building F09, > University of Sydney, NSW 2006 > ______________________________________________ > Phone +61 2 9351 3176 Fax +61 2 9351 7682 > Mobile 0413 281 861 > ______________________________________________ > http://www.guycox.net > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] On > Behalf Of John Oreopoulos > Sent: Sunday, 22 June 2008 10:57 PM > To: [hidden email] > Subject: An alarming amount of image manipulation > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > I was a bit surprised at the statistics cited in this article: > > http://chronicle.com/free/2008/05/3028n.htm > > Does this mean that all journals will start hiring image manipulation > detectives someday? Could be an interesting career. > > > John Oreopoulos, BSc, > PhD Candidate > University of Toronto > Institute For Biomaterials and Biomedical Engineering Centre For Studies > in Molecular Imaging > > Tel: W:416-946-5022 > > No virus found in this incoming message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 > 9:27 AM > > > No virus found in this outgoing message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 > 9:27 AM > > _________________________________________ Michael Cammer http://www.aecom.yu.edu/aif/ |
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Oh for the days of dye-sublimation printers and the tell-tale snail trails of poorly executed "touch-up" jobs. DC -------------------------------------------------- From: "Michael Cammer" <[hidden email]> Sent: Sunday, June 22, 2008 5:30 PM To: <[hidden email]> Subject: Re: An alarming amount of image manipulation > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > In my experience, when somebody shows up with micrographs that have cells > pasted in or background "distractions" stamp tooled out and I suggest > maybe taking more pictures or doing the experiment again, they complain > that this would cost more and delay them. "The data are what they are and > I'm just showing people and if I don't make it look good, then they won't > publish it." Sometimes junior lab members will go back to their PIs and > say that I wasn't helpful; I become the problem. I will not apologize for > refusing to use the lasso tool around a band on a gel and S curve adjust > it in Photoshop Curves or for refusing to paint out "an anomalous bad cell > off in the corner of the image". Yes, both these requests have come > through our facility along with a bunch of other egregious ones. Some > scientists really feel justified because the competition does it. "Hey, > everybody does it," they say. Although, more often (and a search will > show that we've discussed this before), people simply don;t understand > what they are doing. They simply misuse the tools for making figures. As > with example of film, before you can begin to alter images in an > intentional manner or make even reasonably good pictures of anything, you > need to be at least knowledgeable of darkroom technique. But with the new > digital tools, any dummy can be a photographer and can cut and paste and > manipulate in complicated ways. > -Michael > >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> Interesting - especially the statement that images on film >> cannot be doctored. I guess it's irrelevant nowadays, but that >> is so far from the truth. >> >> One funny story - which I've told before but some time ago. >> Many years ago I (with colleagues) published a paper in a >> well-known journal which included a photo of some gels - >> taken by the departmental photographer. One of the gels had >> cracked when it was taken out of the tube, so there was a >> dark hairline across it in the photo. In the published paper >> that line had disappeared. You can hardly accuse me, or my >> two co-authors, of fraud since this was done by the journal's >> art department without any reference to us! >> >> Guy >> >> >> Optical Imaging Techniques in Cell Biology >> by Guy Cox CRC Press / Taylor & Francis >> http://www.guycox.com/optical.htm >> ______________________________________________ >> Associate Professor Guy Cox, MA, DPhil(Oxon) >> Electron Microscope Unit, Madsen Building F09, >> University of Sydney, NSW 2006 >> ______________________________________________ >> Phone +61 2 9351 3176 Fax +61 2 9351 7682 >> Mobile 0413 281 861 >> ______________________________________________ >> http://www.guycox.net >> -----Original Message----- >> From: Confocal Microscopy List [mailto:[hidden email]] On >> Behalf Of John Oreopoulos >> Sent: Sunday, 22 June 2008 10:57 PM >> To: [hidden email] >> Subject: An alarming amount of image manipulation >> >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> I was a bit surprised at the statistics cited in this article: >> >> http://chronicle.com/free/2008/05/3028n.htm >> >> Does this mean that all journals will start hiring image manipulation >> detectives someday? Could be an interesting career. >> >> >> John Oreopoulos, BSc, >> PhD Candidate >> University of Toronto >> Institute For Biomaterials and Biomedical Engineering Centre For Studies >> in Molecular Imaging >> >> Tel: W:416-946-5022 >> >> No virus found in this incoming message. >> Checked by AVG. >> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: >> 21/06/2008 >> 9:27 AM >> >> >> No virus found in this outgoing message. >> Checked by AVG. >> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: >> 21/06/2008 >> 9:27 AM >> >> > > > _________________________________________ > Michael Cammer http://www.aecom.yu.edu/aif/ > > |
David Barnes-2 |
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Good reason why the forensic community is "leary" of Photoshop.
My former company "invented" the tracking process of processes applied circa 1990.
"latentpro" was the most widely used IP package for many years...
On Sun, Jun 22, 2008 at 4:15 PM, Darran Clements <[hidden email]> wrote: Oh for the days of dye-sublimation printers and the tell-tale snail trails of poorly executed "touch-up" jobs. |
ian gibbins |
In reply to this post by John Oreopoulos
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal There is a good article on all this in the most recent edition of Scientific American. It shows how digital image detectives can detect some pretty subtle manipulations. They are mostly looking at press images, but many of the principles apply to microscopy and other lab-generated images. Well worth a read, even if it might take the sparkle from your eye! IAN On Sunday, June 22, 2008, at 10:27 PM, John Oreopoulos wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > I was a bit surprised at the statistics cited in this article: > > http://chronicle.com/free/2008/05/3028n.htm > > Does this mean that all journals will start hiring image manipulation > detectives someday? Could be an interesting career. > > > John Oreopoulos, BSc, > PhD Candidate > University of Toronto > Institute For Biomaterials and Biomedical Engineering > Centre For Studies in Molecular Imaging > > Tel: W:416-946-5022 > > * * * * * * * * * * * Prof Ian Gibbins Anatomy & Histology Flinders University GPO Box 2100 Adelaide SA 5001 AUSTRALIA [hidden email] voice: +61-8-8204 5271 fax: +61-8-8277 0085 http://som.flinders.edu.au/FUSA/Anatomy/ http://www.flinders.edu.au/neuroscience |
Tina Carvalho |
In reply to this post by John Oreopoulos
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal So this might be a good time to remind everyone that the Microscopy Society of America's Education Committee has a subcommittee on the Ethics of Digital Imaging. Several years ago we tackled this problem (intellectually) and came up with amazingly straightforward guidelines: The only thing you can do to a digital image without reporting it as manipulation is changing contrast and brightness, and levels/gamma/curves over the entire image. *Anything* else needs to be reported as an image manipulation in the Materials and Methods. In addition, the original (unmanipulated) image must be stored as an uncompressed TIFF on archival media. It should be available to anyone who requests inspecting the original. We hoped that this would alert (un-educated) researchers to the fact that Photoshoping an image means changing the data, and they would educate themselves about image manipulation programs and how they work and what they are actually dong to an image. Now, of course there are all kinds of things you can do before snapping/saving an image, especially with confocal and fluorescence acquisition software, and we have to rely on people's internal morality meter... But even there researchers should be able to adequately report and describe their software and parameters. If they can't, it's probably more a matter of not understanding what they are doing, a problem that seems to be rampant these days. Of course, there is also the question of deliberate fraud, but I suspect that's truly less that is insinuated in the article and more a question of un-education. Aloha, Tina > I was a bit surprised at the statistics cited in this article: > > http://chronicle.com/free/2008/05/3028n.htm > > Does this mean that all journals will start hiring image manipulation > detectives someday? Could be an interesting career. > > > John Oreopoulos, BSc, > PhD Candidate > University of Toronto > Institute For Biomaterials and Biomedical Engineering > Centre For Studies in Molecular Imaging > > Tel: W:416-946-5022 > **************************************************************************** * Tina (Weatherby) Carvalho * [hidden email] * * Biological Electron Microscope Facility * (808) 956-6251 * * University of Hawaii at Manoa * http://www.pbrc.hawaii.edu/bemf* **************************************************************************** |
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