digital imaging standards
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Does anyone know if there is a "standard" for digital imaging, especially for microscopy related digital imaging? If so, who is in charge of making such a standard? Thank you, Zhaojie Zhang, Ph. D. Director, Jenkins Microscopy Facility University of Wyoming Laramie, WY 82071 PHONE: 307-766-3038 FAX: 307-766-5625 |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I am 99% sure that there is not. Ann -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Z.J. Zhang Sent: Thursday, October 13, 2011 7:29 PM To: [hidden email] Subject: digital imaging standards ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Does anyone know if there is a "standard" for digital imaging, especially for microscopy related digital imaging? If so, who is in charge of making such a standard? Thank you, Zhaojie Zhang, Ph. D. Director, Jenkins Microscopy Facility University of Wyoming Laramie, WY 82071 PHONE: 307-766-3038 FAX: 307-766-5625 |
 
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JOEL B. SHEFFIELD |
Re: digital imaging standards
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** There may not be formal standards, but I would certainly think that there are principles that should guide digital microscopy. 1. The pixel density should correspond, at a minimum, to the relevant detail in the original source. 2. The bit depth should include all levels of intensity in the original --i.e. not saturated, and not clipped. 3. For microscopy, images should include a magnification standard. Any others? On Fri, Oct 14, 2011 at 10:22 AM, Byrne, Ann <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am 99% sure that there is not. > Ann > > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] > On Behalf Of Z.J. Zhang > Sent: Thursday, October 13, 2011 7:29 PM > To: [hidden email] > Subject: digital imaging standards > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Does anyone know if there is a "standard" for digital imaging, > especially for microscopy related digital imaging? > > If so, who is in charge of making such a standard? > > Thank you, > > > Zhaojie Zhang, Ph. D. > Director, Jenkins Microscopy Facility > University of Wyoming > Laramie, WY 82071 > PHONE: 307-766-3038 > FAX: 307-766-5625 > -- Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] URL: http://astro.temple.edu/~jbs |
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John Oreopoulos |
Re: digital imaging standards
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In reply to this post by Byrne, Ann
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Zhaojie, Do you mean standard test samples for diagnosing the "health" of your microscope or proper standards and ethics of digital imaging? For the former, there are several different standards for measuring spatial resolution: sub-diffraction sized fluorescent beads, mirrors, etc. Fluorescent beads can be purchased from many different companies, but there is no agreed upon standard size, dye spectra, or anything like that. Some people have used flow cytometry beads before, and I think the quality control is a bit tighter on those. Molecular Probes also sells a fluorescent bead kit with beads that step up their fluorescent intensity in known amounts (no commercial interest): http://probes.invitrogen.com/media/pis/mp07219.pdf There are also standard resolution targets for brightfield and reflected imaging. Here's an example from Edmund Optics (no commercial interest): http://www.edmundoptics.com/products/displayproduct.cfm?productid=1790 Pawley's confocal handbook says that you can coat these with a fluorescent dye if you want to use them for fluorescence. Unfortunately, there is no intensity standard or "standard candle" for microscopy, although as you may have seen in some recent posts, some people suggest using the transmitted light source of the microscope and a power meter. I think uranyl glass has been talked about several times as well. If someone does have a good intensity standard, I'd really like to know about it as well. If you're talking about digital imaging ethics, there is a fantastic article by Douglas Cromey that throughly discusses the topic: Cromey, D., Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images. Science and Engineering Ethics, 2010. Cheers, John Oreopoulos Research Assistant Spectral Applied Research Richmond Hill, Ontario Canada www.spectral.ca On 2011-10-14, at 10:22 AM, Byrne, Ann wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am 99% sure that there is not. > Ann > > -----Original Message----- > From: Confocal Microscopy List [mailto:[hidden email]] > On Behalf Of Z.J. Zhang > Sent: Thursday, October 13, 2011 7:29 PM > To: [hidden email] > Subject: digital imaging standards > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Does anyone know if there is a "standard" for digital imaging, > especially for microscopy related digital imaging? > > If so, who is in charge of making such a standard? > > Thank you, > > > Zhaojie Zhang, Ph. D. > Director, Jenkins Microscopy Facility > University of Wyoming > Laramie, WY 82071 > PHONE: 307-766-3038 > FAX: 307-766-5625 |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** This may be a good time to mention the ABRF sites comparison, advertised earlier by Claire Brown, and an earlier version published in Microscopy and Microanalysis by Stack et al. They use Chroma fluorescent plastic slides, sub-resolution beads, orange/orange spectral separation beads and reflection off gold coated slide. All good, none perfect. For the health of my SP5 AOBS, I run a daily a 3 minute test that involves x-z-lambda, (occasionally x-z-lambda-t) scanning in reflection mode off a plain glass slide with all lasers on, same parameters of course. It gives a lot of information and it makes it relatively easy to detect problems and pinpoint their sources. Anda -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos Sent: Friday, October 14, 2011 7:55 AM To: [hidden email] Subject: Re: digital imaging standards ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Zhaojie, Do you mean standard test samples for diagnosing the "health" of your microscope or proper standards and ethics of digital imaging? For the former, there are several different standards for measuring spatial resolution: sub-diffraction sized fluorescent beads, mirrors, etc. Fluorescent beads can be purchased from many different companies, but there is no agreed upon standard size, dye spectra, or anything like that. Some people have used flow cytometry beads before, and I think the quality control is a bit tighter on those. Molecular Probes also sells a fluorescent bead kit with beads that step up their fluorescent intensity in known amounts (no commercial interest): http://probes.invitrogen.com/media/pis/mp07219.pdf There are also standard resolution targets for brightfield and reflected imaging. Here's an example from Edmund Optics (no commercial interest): http://www.edmundoptics.com/products/displayproduct.cfm?productid=1790 Pawley's confocal handbook says that you can coat these with a fluorescent dye if you want to use them for fluorescence. Unfortunately, there is no intensity standard or "standard candle" for microscopy, although as you may have seen in some recent posts, some people suggest using the transmitted light source of the microscope and a power meter. I think uranyl glass has been talked about several times as well. If someone does have a good intensity standard, I'd really like to know about it as well. If you're talking about digital imaging ethics, there is a fantastic article by Douglas Cromey that throughly discusses the topic: Cromey, D., Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images. Science and Engineering Ethics, 2010. Cheers, John Oreopoulos Research Assistant Spectral Applied Research Richmond Hill, Ontario Canada www.spectral.ca On 2011-10-14, at 10:22 AM, Byrne, Ann wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > I am 99% sure that there is not. > Ann > > -----Original Message----- > From: Confocal Microscopy List > [mailto:[hidden email]] > On Behalf Of Z.J. Zhang > Sent: Thursday, October 13, 2011 7:29 PM > To: [hidden email] > Subject: digital imaging standards > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Does anyone know if there is a "standard" for digital imaging, > especially for microscopy related digital imaging? > > If so, who is in charge of making such a standard? > > Thank you, > > > Zhaojie Zhang, Ph. D. > Director, Jenkins Microscopy Facility > University of Wyoming > Laramie, WY 82071 > PHONE: 307-766-3038 > FAX: 307-766-5625 |
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In reply to this post by Z.J. Zhang
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi All, ISO The International Organization for Standardization covers this. http://www.iso.org/iso/search.htm? qt=digital+image&sort=rel&type=simple&published=on Along with many standards for Microscopy. http://www.iso.org/iso/search.htm? qt=microscopy&sort=rel&type=simple&published=on Of which I am a committee member Stan Schwartz Nikon Instruments Inc |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hey Stan/all No offense meant but I find your wording "many standards" somewhat puzzling! Shouldn't it be the meaning of a "standard" to be a unique, approved and shared reference? I haven't been there in a while but there may/should be a reflexion group on this in the EuroBioImaging initiative!? Eric Ps. I am surprised that all the document at the ISO are only accessible on a pay basis! Eric Scarfone, PhD, CNRS, Cell: +46 (0)70 888 2352 email: [hidden email] > -----Original Message----- > From: Confocal Microscopy List > [mailto:[hidden email]] On Behalf Of Stan Schwartz > Sent: 15 October 2011 15:15 > To: [hidden email] > Subject: Re: digital imaging standards > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Hi All, > > ISO The International Organization for Standardization covers this. > > http://www.iso.org/iso/search.htm? > qt=digital+image&sort=rel&type=simple&published=on > > Along with many standards for Microscopy. > http://www.iso.org/iso/search.htm? > qt=microscopy&sort=rel&type=simple&published=on > > Of which I am a committee member > > Stan Schwartz > Nikon Instruments Inc |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** > No offense meant but I find your wording "many standards" somewhat > puzzling! > Shouldn't it be the meaning of a "standard" to be a unique, approved and > shared reference? > I haven't been there in a while but there may/should be a reflexion group > on this in the EuroBioImaging initiative!? > Eric > > Ps. I am surprised that all the document at the ISO are only accessible on > a pay basis! > the standards cover different aspects of microscopy. but I agree that having to pay is a problem and it has disturbed me for a long time. it's fine if you work for a company; but me, when I'm doing volunteer-work coding open source, I think I should have free access to them /Johan > > > Eric Scarfone, PhD, CNRS, > > Cell: +46 (0)70 888 2352 > email: [hidden email] > > > > -----Original Message----- > > From: Confocal Microscopy List > > [mailto:[hidden email]] On Behalf Of Stan Schwartz > > Sent: 15 October 2011 15:15 > > To: [hidden email] > > Subject: Re: digital imaging standards > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > ***** > > > > Hi All, > > > > ISO The International Organization for Standardization covers this. > > > > http://www.iso.org/iso/search.htm? > > qt=digital+image&sort=rel&type=simple&published=on > > > > Along with many standards for Microscopy. > > http://www.iso.org/iso/search.htm? > > qt=microscopy&sort=rel&type=simple&published=on > > > > Of which I am a committee member > > > > Stan Schwartz > > Nikon Instruments Inc > -- ----------------------------------------------------------- Johan Henriksson PhD student, Karolinska Institutet http://mahogny.areta.org http://www.endrov.net |
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In reply to this post by Z.J. Zhang
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** MIAWiki, Wiki for Microscopy and Image Analysis, is a collaboration tool where primary information like papers, patents, etc. can be cited, analysed, published and shared for free. In many cases R&D is based on the best practices and protocols rather than standards. Please discover capabilities of MIAWiki of real time accumulation and finding knowledge on your current demand. http://confocal-manawatu.pbworks.com/w/page/16346911/FrontPage Sincerely, Dmitry |
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In reply to this post by Z.J. Zhang
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Another take on this subject is: imaging performance standards which we working on ( <http://www.abrf.org/index.cfm/group.show/LightMicroscopyResearchGroup.54.ht m> http://www.abrf.org/index.cfm/group.show/LightMicroscopyResearchGroup.54.htm ). Our last publication summarize the first part. Stack, R., Bayles, C., Girard, A., Martin, K., Opansky, C., Schulz, K., and Cole, R. (2011) Quality Assurance Testing for Modern Optical Imaging Systems. Microscopy & Microanalysis 17(4):598-606. Rich Richard Cole Research Scientist V Director: Advanced Light Microscopy & Image Analysis Core Wadsworth Center P.O. Box 509 Albany N.Y. 12201-0509 Research Assistant Professor Dept. of Biomedical Sciences School of Public Health State University of New York Albany, New York ( 518-474-7048 Ê 518-474-4430 * <mailto:[hidden email]> [hidden email] Website www.wadsworth.org/cores/alm/index.htm IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation. |
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