Re: Automation of microscopy?
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John Oreopoulos |
Re: Automation of microscopy?
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A very interesting commentary on this topic appeared recently in the journal listed below. I'd like to ask the community again if they think this is where microscopy is headed. Title: High-throughput microscopy must re-invent the microscope rather than speed up its functions Authors: Oheim, M Source: BRITISH JOURNAL OF PHARMACOLOGY 152 (1): 1-4 SEP 2007 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 On 16-May-07, at 1:35 PM, Ed Monosov wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Judy, |
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George McNamara |
Re: Automation of microscopy?
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Search the CONFOCAL archive at
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Hi John, No. It's been there years. Most biomedical researchers do not need any of this. As for the closing paragraph's, "One crucial question is: will automated microscopy remain the realm of large consortia and imaging platforms that combine transversal expertise in a tight and large-scale academicindustrial partnership, or will it, via commercial products, make its way into the small- and medium-sized laboratories to fundamentally change the way fluorescence imaging is done today in cell biological research?" My first involvement in N-dimensional automated microscopy was an Image-1/AT calcium imaging system on a Nikon inverted microscope, temperature controlled environment, motorized focus, filter wheel, shutter, CCD camera, in 1990 in a medium sized lab. UIC and its dealers had been selling such systems for years, as had other companies. The key fundamental technology at that time was not the hardware, but, rather, fura-2/AM. My first experience with automated microscopy was with a timelapse acquisition system 1981. As for the author's statement, "surprisingly little effort has gone into miniaturizing and streamlining the microscope core itself", the nondescanned detectors on many multiphoton microscopes are already as streamlined as possible. How productive have user's of the Till iMIC and LaVision's TriMScope have been? What new discoveries have been made with either platform? I have been underwhelmed by both as far as practical use. By comparison, I am a fan of AMNIS's imaging in flow approach (not that it has been used to make any stunning new discoveries to date). I was happy to see that both Oheim's and Starkuviene & Pepperkok's articles are free access. George At 03:29 PM 9/28/2007, you wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal George McNamara, Ph.D. University of Miami, Miller School of Medicine Image Core Miami, FL 33010 [hidden email] [hidden email] 305-243-8436 office |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal George & others, Having seen up close how poorly the average grad student & post-doc do "low throughput" microscopy, all I can imagine with high-throughput is the ability to gather semi-meaningful data faster. Surely higher through-put for screening would be great for specific applications, but the thought of something like this being in the hands of people who treat it like a magic black box worries me. Under the microscope: The use of 'black box' techniques carries risks. Nature 447, 116 (10 May 2007) http://www.nature.com/nature/journal/v447/n7141/full/447116a.html Doug George McNamara wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > Hi John, > > No. It's been there years. Most biomedical researchers do not need any > of this. > > As for the closing paragraph's, > > "One crucial question is: will automated microscopy remain the realm > of large consortia and imaging platforms that combine transversal > expertise in a tight and large-scale academic–industrial partnership, > or will it, via commercial products, make its way into the small- and > medium-sized laboratories to fundamentally change the way fluorescence > imaging is done today in cell biological research?" > > My first involvement in N-dimensional automated microscopy was an > Image-1/AT calcium imaging system on a Nikon inverted microscope, > temperature controlled environment, motorized focus, filter wheel, > shutter, CCD camera, in 1990 in a medium sized lab. UIC and its > dealers had been selling such systems for years, as had other > companies. The key fundamental technology at that time was not the > hardware, but, rather, fura-2/AM. My first experience with automated > microscopy was with a timelapse acquisition system 1981. > > As for the author's statement, "surprisingly little effort has gone > into miniaturizing and streamlining the microscope core itself", the > nondescanned detectors on many multiphoton microscopes are already as > streamlined as possible. > > How productive have user's of the Till iMIC and LaVision's TriMScope > have been? What new discoveries have been made with either platform? I > have been underwhelmed by both as far as practical use. By comparison, > I am a fan of AMNIS's imaging in flow approach (not that it has been > used to make any stunning new discoveries to date). > > I was happy to see that both Oheim's and Starkuviene & Pepperkok's > articles are free access. > > George > > > > At 03:29 PM 9/28/2007, you wrote: >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> A very interesting commentary on this topic appeared recently in the >> journal listed below. I'd like to ask the community again if they >> think this is where microscopy is headed. >> >> Title: >> High-throughput microscopy must re-invent the microscope rather than >> speed up its functions >> >> Authors: >> Oheim, M >> >> Source: >> BRITISH JOURNAL OF PHARMACOLOGY 152 (1): 1-4 SEP 2007 >> >> >> 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 >> >> >> >> On 16-May-07, at 1:35 PM, Ed Monosov wrote: >> >>> Search the CONFOCAL archive at >>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Judy, >>> >>> You made my day, or month, or years. >>> Nobody said better than you and Leonardo. >>> With your permission I'll post your email on my web page and I'll >>> also post the Leonardo's wisdom besides all our microscopes. >>> I hope people will read them >>> >>> With all my respect, >>> >>> Ed >>> >>> >>> Judy Trogadis wrote: >>>> >>>> Search the CONFOCAL archive at >>>> >>>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >>>> >>>> I'm replying because of my experience, not because of my age :-) >>>> >>>> Some of the replies to this query have elegantly oulined arguments on >>>> the dangers of hyper-automation during image capture. I would like to >>>> add the importance of actually sitting and studying a preparation or a >>>> set of collected images. Simply put - the longer you look, the more you >>>> see. You have to become familiar with the data, to know the range of >>>> variability and then manually adjust settings so the captured images >>>> truly represent what you see and answer your specific question. >>>> >>>> This can be extended to the analysis as well. Users these days have >>>> a >>>> 'kit'-like mentality, follow the instructions and you will get results. >>>> But if you haven't reviewed the images several times, you may have >>>> missed a subtle, yet critical observation. I try to encourage users to >>>> look for creative ways of analyzing the data, it's more fun (and gets >>>> easier into journals). >>>> >>>> I have a sign posted beside one of the confocals, a quote attributed to >>>> Leonardo Da Vinci >>>> "It's not enough to believe what you see, you must also understand >>>> what >>>> you see." >>>> >>>> Judy >>>> >>>> >>>> Judy Trogadis >>>> Bio-Imaging Coordinator >>>> St. Michael's Hospital, 7Queen >>>> 30 Bond St. >>>> Toronto, ON M5B 1W8, Canada >>>> ph: 416-864-6060 x6337 >>>> pager: 416-685-9219 >>>> fax: 416-864-6043 >>>> >>>> [hidden email] <mailto:[hidden email]> >>>> >>>> >>>> >>>> >>>>>>> >>>>>>> >>>>>>> [hidden email] <mailto:[hidden email]> 05/15/07 10:02 AM >>> >>>>>>> >>>>>>> >>>> >>>> Search the CONFOCAL archive at >>>> >>>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >>>> >>>> >>>> I'm very curious to know from some of the older and more >>>> experienced >>>> microscopists out there what they think about this trend, ie: I've >>>> seen that the newest models of the confocal microscope that we have >>>> (which is about ten years old now) comes with all sorts of buttons >>>> that flip the filters and focus the image automatically, etc. Is this >>>> >>>> really a good thing for microscopy, or, as the article points out, is >>>> >>>> it possible that it promotes sloppy image collection? >>>> >>>> >>>> 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 >>>> >>>> >>>> >>> >>> >>> -- >>> Edward Monosov, Ph.D. >>> Director , Cell Imaging & Histology >>> BURNHAM INSTITUTE for MEDICAL RESEARCH >>> 10901 N. Torrey Pines Rd, >>> La Jolla, CA 92037 >>> Ph: (858)646-3100 ext. 3206 >>> Fax: (858)646-3196 >>> [hidden email] <mailto:[hidden email]> >>> >> >> >> > > > > > > George McNamara, Ph.D. > University of Miami, Miller School of Medicine > Image Core > Miami, FL 33010 > [hidden email] > [hidden email] > 305-243-8436 office > > -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Douglas W. Cromey, M.S. - Assistant Scientific Investigator Dept. of Cell Biology & Anatomy, University of Arizona 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA office: AHSC 4212 email: [hidden email] voice: 520-626-2824 fax: 520-626-2097 http://swehsc.pharmacy.arizona.edu/exppath/ Home of: "Microscopy and Imaging Resources on the WWW" |
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In reply to this post by George McNamara
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Sorry, haven't had a chance to read this thread earlier - words like "high-throughput" and "screening" implies to me that you already know what you're looking for. That's great when you're at the hypothesis testing stage, but how does that help you find a new observation? Furthermore, once you acquire a lot of data very quickly, you still have to analyze it - accurately and honestly. Judy Judy Trogadis Bio-Imaging Coordinator St. Michael's Hospital, 7Queen 30 Bond St. Toronto, ON M5B 1W8, Canada ph: 416-864-6060 x6337 pager: 416-685-9219 fax: 416-864-6043 [hidden email] >>> George McNamara <[hidden email]> 09/29/07 2:14 PM >>> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi John, No. It's been there years. Most biomedical researchers do not need any of this. As for the closing paragraph's, "One crucial question is: will automated microscopy remain the realm of large consortia and imaging platforms that combine transversal expertise in a tight and large-scale academic*industrial partnership, or will it, via commercial products, make its way into the small- and medium-sized laboratories to fundamentally change the way fluorescence imaging is done today in cell biological research?" My first involvement in N-dimensional automated microscopy was an Image-1/AT calcium imaging system on a Nikon inverted microscope, temperature controlled environment, motorized focus, filter wheel, shutter, CCD camera, in 1990 in a medium sized lab. UIC and its dealers had been selling such systems for years, as had other companies. The key fundamental technology at that time was not the hardware, but, rather, fura-2/AM. My first experience with automated microscopy was with a timelapse acquisition system 1981. As for the author's statement, "surprisingly little effort has gone into miniaturizing and streamlining the microscope core itself", the nondescanned detectors on many multiphoton microscopes are already as streamlined as possible. How productive have user's of the Till iMIC and LaVision's TriMScope have been? What new discoveries have been made with either platform? I have been underwhelmed by both as far as practical use. By comparison, I am a fan of AMNIS's imaging in flow approach (not that it has been used to make any stunning new discoveries to date). I was happy to see that both Oheim's and Starkuviene & Pepperkok's articles are free access. George At 03:29 PM 9/28/2007, you wrote: >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >A very interesting commentary on this topic >appeared recently in the journal listed below. >I'd like to ask the community again if they >think this is where microscopy is headed. > >Title: >High-throughput microscopy must re-invent the >microscope rather than speed up its functions > >Authors: >Oheim, M > >Source: >BRITISH JOURNAL OF PHARMACOLOGY 152 (1): 1-4 SEP 2007 > > >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 > > > >On 16-May-07, at 1:35 PM, Ed Monosov wrote: > >>Search the CONFOCAL archive at >><http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >>Dear Judy, >> >>You made my day, or month, or years. >>Nobody said better than you and Leonardo. >>With your permission I'll post your email on my >>web page and I'll also post the Leonardo's wisdom besides all our microscopes. >>I hope people will read them >> >>With all my respect, >> >>Ed >> >> >>Judy Trogadis wrote: >>> >>>Search the CONFOCAL archive at >>><http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >>> >>>I'm replying because of my experience, not because of my age :-) >>> >>>Some of the replies to this query have elegantly oulined arguments on >>>the dangers of hyper-automation during image capture. I would like to >>>add the importance of actually sitting and studying a preparation or a >>>set of collected images. Simply put - the longer you look, the more you >>>see. You have to become familiar with the data, to know the range of >>>variability and then manually adjust settings so the captured images >>>truly represent what you see and answer your specific question. >>> >>>This can be extended to the analysis as well. Users these days have a >>>'kit'-like mentality, follow the instructions and you will get results. >>>But if you haven't reviewed the images several times, you may have >>>missed a subtle, yet critical observation. I try to encourage users to >>>look for creative ways of analyzing the data, it's more fun (and gets >>>easier into journals). >>> >>>I have a sign posted beside one of the confocals, a quote attributed to >>>Leonardo Da Vinci >>>"It's not enough to believe what you see, you must also understand what >>>you see." >>> >>>Judy >>> >>> >>>Judy Trogadis >>>Bio-Imaging Coordinator >>>St. Michael's Hospital, 7Queen >>>30 Bond St. >>>Toronto, ON M5B 1W8, Canada >>>ph: 416-864-6060 x6337 >>>pager: 416-685-9219 >>>fax: 416-864-6043 >>><mailto:[hidden email]>[hidden email] >>> >>> >>> >>>>>> >>>>>><mailto:[hidden email]>[hidden email] >>>>>>05/15/07 10:02 AM >>> >>>>>> >>> >>>Search the CONFOCAL archive at >>><http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >>> >>> >>> >>>I'm very curious to know from some of the older and more experienced >>>microscopists out there what they think about this trend, ie: I've >>>seen that the newest models of the confocal microscope that we have >>>(which is about ten years old now) comes with all sorts of buttons >>>that flip the filters and focus the image automatically, etc. Is this >>> >>>really a good thing for microscopy, or, as the article points out, is >>> >>>it possible that it promotes sloppy image collection? >>> >>> >>>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 >>> >>> >> >> >>-- >>Edward Monosov, Ph.D. >>Director , Cell Imaging & Histology >>BURNHAM INSTITUTE for MEDICAL RESEARCH >>10901 N. Torrey Pines Rd, >>La Jolla, CA 92037 >>Ph: (858)646-3100 ext. 3206 >>Fax: (858)646-3196 >><mailto:[hidden email]>[hidden email] > > > George McNamara, Ph.D. University of Miami, Miller School of Medicine Image Core Miami, FL 33010 [hidden email] [hidden email] 305-243-8436 office |
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Armstrong, Brian |
Re: Automation of microscopy?
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Judy, the latest HTS systems are really quite impressive especially with regards to the data handling/mining/quantitation. As you point out this may be the salient feature of these systems. I have seen many demos recently and have been impressed. Don't dismiss this genre without evaluation. Cheers, http://www.evotec.com http://www.cellomics.com/ http://www.bdbiosciences.com/nvCategory.jsp?item=648444&action=SELECT&fo rm=formTree_catBean http://www.moleculardevices.com/ Brian D Armstrong PhD Light Microscopy Core Manager Beckman Research Institute City of Hope 1450 E Duarte Rd Duarte, CA 91010 626-359-8111 x62872 http://www.cityofhope.org/SharedResources/LightMicroscopy -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Judy Trogadis Sent: Tuesday, October 09, 2007 7:20 AM To: [hidden email] Subject: Re: Automation of microscopy? Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Sorry, haven't had a chance to read this thread earlier - words like "high-throughput" and "screening" implies to me that you already know what you're looking for. That's great when you're at the hypothesis testing stage, but how does that help you find a new observation? Furthermore, once you acquire a lot of data very quickly, you still have to analyze it - accurately and honestly. Judy Judy Trogadis Bio-Imaging Coordinator St. Michael's Hospital, 7Queen 30 Bond St. Toronto, ON M5B 1W8, Canada ph: 416-864-6060 x6337 pager: 416-685-9219 fax: 416-864-6043 [hidden email] >>> George McNamara <[hidden email]> 09/29/07 2:14 PM >>> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi John, No. It's been there years. Most biomedical researchers do not need any of this. As for the closing paragraph's, "One crucial question is: will automated microscopy remain the realm of large consortia and imaging platforms that combine transversal expertise in a tight and large-scale academic*industrial partnership, or will it, via commercial products, make its way into the small- and medium-sized laboratories to fundamentally change the way fluorescence imaging is done today in cell biological research?" My first involvement in N-dimensional automated microscopy was an Image-1/AT calcium imaging system on a Nikon inverted microscope, temperature controlled environment, motorized focus, filter wheel, shutter, CCD camera, in 1990 in a medium sized lab. UIC and its dealers had been selling such systems for years, as had other companies. The key fundamental technology at that time was not the hardware, but, rather, fura-2/AM. My first experience with automated microscopy was with a timelapse acquisition system 1981. As for the author's statement, "surprisingly little effort has gone into miniaturizing and streamlining the microscope core itself", the nondescanned detectors on many multiphoton microscopes are already as streamlined as possible. How productive have user's of the Till iMIC and LaVision's TriMScope have been? What new discoveries have been made with either platform? I have been underwhelmed by both as far as practical use. By comparison, I am a fan of AMNIS's imaging in flow approach (not that it has been used to make any stunning new discoveries to date). I was happy to see that both Oheim's and Starkuviene & Pepperkok's articles are free access. George At 03:29 PM 9/28/2007, you wrote: >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >A very interesting commentary on this topic >appeared recently in the journal listed below. >I'd like to ask the community again if they >think this is where microscopy is headed. > >Title: >High-throughput microscopy must re-invent the >microscope rather than speed up its functions > >Authors: >Oheim, M > >Source: >BRITISH JOURNAL OF PHARMACOLOGY 152 (1): 1-4 SEP 2007 > > >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 > > > >On 16-May-07, at 1:35 PM, Ed Monosov wrote: > >>Search the CONFOCAL archive at >><http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>http://listse >>Dear Judy, >> >>You made my day, or month, or years. >>Nobody said better than you and Leonardo. >>With your permission I'll post your email on my >>web page and I'll also post the Leonardo's wisdom besides all our microscopes. >>I hope people will read them >> >>With all my respect, >> >>Ed >> >> >>Judy Trogadis wrote: >>> >>>Search the CONFOCAL archive at >>><http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>http://lists >>> >>>I'm replying because of my experience, not because of my age :-) >>> >>>Some of the replies to this query have elegantly oulined arguments on >>>the dangers of hyper-automation during image capture. I would like to >>>add the importance of actually sitting and studying a preparation or a >>>set of collected images. Simply put - the longer you look, the more you >>>see. You have to become familiar with the data, to know the range of >>>variability and then manually adjust settings so the captured images >>>truly represent what you see and answer your specific question. >>> >>>This can be extended to the analysis as well. Users these days have a >>>'kit'-like mentality, follow the instructions and you will get results. >>>But if you haven't reviewed the images several times, you may have >>>missed a subtle, yet critical observation. I try to encourage users to >>>look for creative ways of analyzing the data, it's more fun (and gets >>>easier into journals). >>> >>>I have a sign posted beside one of the confocals, a quote attributed to >>>Leonardo Da Vinci >>>"It's not enough to believe what you see, you must also understand what >>>you see." >>> >>>Judy >>> >>> >>>Judy Trogadis >>>Bio-Imaging Coordinator >>>St. Michael's Hospital, 7Queen >>>30 Bond St. >>>Toronto, ON M5B 1W8, Canada >>>ph: 416-864-6060 x6337 >>>pager: 416-685-9219 >>>fax: 416-864-6043 >>><mailto:[hidden email]>[hidden email] >>> >>> >>> >>>>>> >>>>>><mailto:[hidden email]>[hidden email] >>>>>>05/15/07 10:02 AM >>> >>>>>> >>> >>>Search the CONFOCAL archive at >>><http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>http://lists >>> >>> >>> >>>I'm very curious to know from some of the older and more experienced >>>microscopists out there what they think about this trend, ie: I've >>>seen that the newest models of the confocal microscope that we have >>>(which is about ten years old now) comes with all sorts of buttons >>>that flip the filters and focus the image automatically, etc. Is this >>> >>>really a good thing for microscopy, or, as the article points out, is >>> >>>it possible that it promotes sloppy image collection? >>> >>> >>>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 >>> >>> >> >> >>-- >>Edward Monosov, Ph.D. >>Director , Cell Imaging & Histology >>BURNHAM INSTITUTE for MEDICAL RESEARCH >>10901 N. Torrey Pines Rd, >>La Jolla, CA 92037 >>Ph: (858)646-3100 ext. 3206 >>Fax: (858)646-3196 >><mailto:[hidden email]>[hidden email] > > > George McNamara, Ph.D. University of Miami, Miller School of Medicine Image Core Miami, FL 33010 [hidden email] [hidden email] 305-243-8436 office "EMF <COH.org>" made the following annotations. ------------------------------------------------------------------------------ SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. 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