seeking "reliable literature" on correct imaging
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Sylvie Le Guyader |
Re: seeking "reliable literature" on correct imaging
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Michael On our website<https://ki.se/en/bionut/welcome-to-the-lci-facility> (under Learning microscopy/Teaching material) you can find links to our Youtube videos which are freely available. One of them talks about bleedthrough and channel crosstalk. Another one talks about bit depth, saturation and underexposure. I realize that the sound of that video is a bit jumpy and that there is a mistake (the file size does not increase exponentially with the bit depth, it only doubles between 8 and 16 bits). Unfortunately it is not possible anymore to add annotation to Youtube videos. We will record it again but the rest of the information is correct and, I hope, clear and useful. We are in the process of making one more video about the importance of choosing the correct objective and setting the correct pixel size in relation to the sample/scientific question. Above the video there is a file that might also be useful. It is called ‘Typical workflow of how to set a confocal’ which we use as a frame for our confocal training. Additionally we are running a microscopy course in January/February. The schedule is available on the same page as the videos. All the lectures are broadcasted live as long as the speakers agree. Instructions on how to connect will be set up on the same webpage shortly before the course. Feel free to use all this material. Please acknowledge our facility. :) Med vänlig hälsning / Best regards Sylvie @@@@@@@@@@@@@@@@@@@@@@@@ Sylvie Le Guyader, PhD Live Cell Imaging Facility Manager Karolinska Institutet- Bionut Dpt Hälsovägen 7C, Room 7362 (lab)/7840 (office) 14157 Huddinge, Sweden mobile: +46 (0) 73 733 5008 LCI website<https://ki.se/en/bionut/welcome-to-the-lci-facility> Follow our microscopy blog<http://microscopykarolinska.se/>! Am 16.11.2018 um 17:50 schrieb Cammer, Michael: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Increasingly we have found that microscope users do not understand proper imaging. > > A few examples: > Confocal images are saturated and have the offset set to negative numbers intentionally "to reduce background". > Exposures are changed in fluorescent micrographs to make each one "look good". > 16 bit raw data with no saturation or clipping are set to 8 bits with a lot of saturated and clipped pixels at the extremes and these are what are considered raw data. > JPG compression is great because images can be emailed. > People assume (and get angry when this doesn't work) that computers can automatically segment and count anything regardless of experimental design, image quality, etc. > Even if they have saved everything as TIF with no metadata and forgot what magnifications they used. > > A student who recognizes these problems and wants to learn the right way emailed me yesterday asking for "any reliable literature you recommend if I'd like to read more about correct imaging." > > I did Google searches and, after skimming a bunch of web pages, realized that I didn't really have an answer. I could send to this page and to this page, but it's not a coherent narrative. And I don't have a library; most of what I know about this was picked up willy-nilly up in the 1980s and '90s. For instance knowledge of color separation from writing animations for the Apple II in machine code, working in a cable TV studio in the 1980s, and from an art history class in college where we discussed 19th C travel photos and poly/monochromatic film chemistries of the periods. Later I learned fluorescence quantification from a cell biologist intent on making sure we had true linear responses for readouts of f-actin mass and concentration, I was fortunate to attend both a Woods Hole microscopy course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 training course at their offices in Cambridge, MA covered a lot of material on this too. > > So, do people have favorite texts that cover these topics in a manner digestible by new generations of students? Of biology students. Keep in mind many don't know what a byte is; when I teach I ask the class if anyone knows why an image is coded with white as 255 or 4095 or 16383 and typically one or two hands go up but the rest of the class really doesn't know. > Looking forward to suggestions of easy to read definitive texts! > > Thank you. > > Cheers- > > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. > ================================= > -- ------------------------------------------------------------ Steffen Dietzel, PD Dr. rer. nat Ludwig-Maximilians-Universität München Biomedical Center (BMC) Head of the Core Facility Bioimaging Großhaderner Straße 9 D-82152 Planegg-Martinsried Germany http://www.bioimaging.bmc.med.uni-muenchen.de När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. |
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In reply to this post by Rosemary.White
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** https://www.dropbox.com/sh/00a8rb2ltxr4d1y/AACCQI8grT5FGz5KnuFqJTgKa?dl=0 Hi Rosemary, Here is a link. And thanks for the suggestion. It's about a few things that can be measured with a microscope. I don't know if that could be made into a reasonably short and useful review. But if you decide to write such a paper and would like to me contribute a little, I would be glad to. Best wishes Mike -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of [hidden email] Sent: Sunday, November 18, 2018 7:07 PM To: [hidden email] Subject: Re: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Mike, I have given talks like this in the rather dim past, but would be very interested in a copy of your Powerpoint file. Maybe you might have time to make it into a small (review) paper? One of the microscopy journals might publish it - e.g. Journal of Microscopy(?) thanks, Rosemary Dr Rosemary White CSIRO Black Mountain GPO Box 1700 Canberra, ACT 2601 Australia T 61 2 6246 5475 M 61 468 966 713 ________________________________________ From: Confocal Microscopy List [[hidden email]] on behalf of MODEL, MICHAEL [[hidden email]] Sent: Saturday, 17 November 2018 4:00 a.m. To: [hidden email] Subject: Re: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Michael, We recently ran a workshop where I gave a 3-hour talk on various kinds of quantification in microscopy. I can send you a PowerPoint file but don't have a text. Mike Model -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of Cammer, Michael Sent: Friday, November 16, 2018 11:50 AM To: [hidden email] Subject: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Increasingly we have found that microscope users do not understand proper imaging. A few examples: Confocal images are saturated and have the offset set to negative numbers intentionally "to reduce background". Exposures are changed in fluorescent micrographs to make each one "look good". 16 bit raw data with no saturation or clipping are set to 8 bits with a lot of saturated and clipped pixels at the extremes and these are what are considered raw data. JPG compression is great because images can be emailed. People assume (and get angry when this doesn't work) that computers can automatically segment and count anything regardless of experimental design, image quality, etc. Even if they have saved everything as TIF with no metadata and forgot what magnifications they used. A student who recognizes these problems and wants to learn the right way emailed me yesterday asking for "any reliable literature you recommend if I'd like to read more about correct imaging." I did Google searches and, after skimming a bunch of web pages, realized that I didn't really have an answer. I could send to this page and to this page, but it's not a coherent narrative. And I don't have a library; most of what I know about this was picked up willy-nilly up in the 1980s and '90s. For instance knowledge of color separation from writing animations for the Apple II in machine code, working in a cable TV studio in the 1980s, and from an art history class in college where we discussed 19th C travel photos and poly/monochromatic film chemistries of the periods. Later I learned fluorescence quantification from a cell biologist intent on making sure we had true linear responses for readouts of f-actin mass and concentration, I was fortunate to attend both a Woods Hole microscopy course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 training course at their offices in Cambridge, MA covered a lot of material on this too. So, do people have favorite texts that cover these topics in a manner digestible by new generations of students? Of biology students. Keep in mind many don't know what a byte is; when I teach I ask the class if anyone knows why an image is coded with white as 255 or 4095 or 16383 and typically one or two hands go up but the rest of the class really doesn't know. Looking forward to suggestions of easy to read definitive texts! Thank you. Cheers- ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= |
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Julia Edgar |
Re: seeking "reliable literature" on correct imaging
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In reply to this post by Karissa Tilbury
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. Best wishes Julia Sent from my iPhone. Please excuse typos. > On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Mike, > > I too would also appreciate this PowerPoint. I think in the context of the > ethics thread, this is very interesting and useful conversation. My > students are currently in the mandated ethics class and the topics > discussed are crazy extremes that really have their roots in 'smaller' less > obvious mistakes to most people. Focusing the discussion on what they are > doing in the lab to protect the quality of data or understand limitations > seems more important to me, than discussing ethics of CRISPR and human > life. > > Karissa > > On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor <[hidden email] > wrote: > >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> Post images on http://www.imgur.com and include the link in your posting. >> ***** >> >> Hi >> I do visit various institutions to teach basics on microscopy and imaging >> always struggle convey the right message in the absence of a proper >> material.. >> Your presentation may be really a good tool for me to convey correct >> message and make the next generation scientist fool proof.. >> Kindly provide me the PPT .. >> Reg >> Ganesh Kadasoor >> Bangalore >> India >> >> >> Sent from my iPhone >> >>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> >> wrote: >>> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your >> posting. >>> ***** >>> >>> Hi Mike, >>> >>> I would like a copy of the PowerPoint as well. This is a very important >> issue that Michael Cammer raises. Trainees (and even more senior folks) >> continue to make these mistakes even as you emphatically tell them not to. >>> >>> Thanks again, >>> >>> John >>> >>> -- >>> John J. Lemasters, MD, PhD >>> Professor and GlaxoSmithKline Distinguished Endowed Chair >>> Director, Center for Cell Death, Injury & Regeneration >>> Departments of Drug Discovery & Biomedical Sciences and Biochemistry & >> Molecular Biology >>> Medical University of South Carolina >>> DD504 Drug Discovery Building >>> 70 President Street, MSC 139 >>> Charleston, SC 29425 >>> >>> Office: 843-876-2360 >>> Lab: 843-876-2354 >>> Fax: 843-876-2353 >>> Email: [hidden email] >>> http://academicdepartments.musc.edu/ccdir >>> >>> -----Original Message----- >>> From: Confocal Microscopy List [mailto:[hidden email]] >> On Behalf Of Kathryn Spencer >>> Sent: Friday, November 16, 2018 12:32 PM >>> To: [hidden email] >>> Subject: Re: seeking "reliable literature" on correct imaging >>> >>> CAUTION: External >>> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your >> posting. >>> ***** >>> >>> Hi Mike; >>> Could I get your PowerPoint as well? I have the same issues with >> my users. I'm "retraining" all of them with an open-software quiz, to see >> if they understand basic concepts. Many are complaining and reluctant, >> because they don't see the issues with their images. This after one 6-year >> post-doc's data was totally discarded because she saved everything as >> JPG....I certainly NEVER taught her to do THAT. >>> Your PowerPoint should hold more credibility that I obviously >> have.... >>> Best; >>> Kathy >>> >>> >>> >>> -----Original Message----- >>> From: Confocal Microscopy List <[hidden email]> On >> Behalf Of MODEL, MICHAEL >>> Sent: Friday, November 16, 2018 9:00 AM >>> To: [hidden email] >>> Subject: Re: seeking "reliable literature" on correct imaging >>> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your >> posting. >>> ***** >>> >>> Hi Michael, >>> >>> We recently ran a workshop where I gave a 3-hour talk on various kinds >> of quantification in microscopy. I can send you a PowerPoint file but don't >> have a text. >>> >>> Mike Model >>> >>> -----Original Message----- >>> From: Confocal Microscopy List <[hidden email]> On >> Behalf Of Cammer, Michael >>> Sent: Friday, November 16, 2018 11:50 AM >>> To: [hidden email] >>> Subject: seeking "reliable literature" on correct imaging >>> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your >> posting. >>> ***** >>> >>> Increasingly we have found that microscope users do not understand >> proper imaging. >>> >>> A few examples: >>> Confocal images are saturated and have the offset set to negative >> numbers intentionally "to reduce background". >>> Exposures are changed in fluorescent micrographs to make each one "look >> good". >>> 16 bit raw data with no saturation or clipping are set to 8 bits with a >> lot of saturated and clipped pixels at the extremes and these are what are >> considered raw data. >>> JPG compression is great because images can be emailed. >>> People assume (and get angry when this doesn't work) that computers can >> automatically segment and count anything regardless of experimental design, >> image quality, etc. >>> Even if they have saved everything as TIF with no metadata and forgot >> what magnifications they used. >>> >>> A student who recognizes these problems and wants to learn the right way >> emailed me yesterday asking for "any reliable literature you recommend if >> I'd like to read more about correct imaging." >>> >>> I did Google searches and, after skimming a bunch of web pages, realized >> that I didn't really have an answer. I could send to this page and to this >> page, but it's not a coherent narrative. And I don't have a library; most >> of what I know about this was picked up willy-nilly up in the 1980s and >> '90s. For instance knowledge of color separation from writing animations >> for the Apple II in machine code, working in a cable TV studio in the >> 1980s, and from an art history class in college where we discussed 19th C >> travel photos and poly/monochromatic film chemistries of the periods. >> Later I learned fluorescence quantification from a cell biologist intent on >> making sure we had true linear responses for readouts of f-actin mass and >> concentration, I was fortunate to attend both a Woods Hole microscopy >> course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 >> training course at their offices in Cambridge, MA covered a lot of material >> on this too. >>> >>> So, do people have favorite texts that cover these topics in a manner >> digestible by new generations of students? Of biology students. Keep in >> mind many don't know what a byte is; when I teach I ask the class if anyone >> knows why an image is coded with white as 255 or 4095 or 16383 and >> typically one or two hands go up but the rest of the class really doesn't >> know. >>> Looking forward to suggestions of easy to read definitive texts! >>> >>> Thank you. >>> >>> Cheers- >>> >>> >>> ------------------------------------------------------------ >>> This email message, including any attachments, is for the sole use of >> the intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check >> this email and any attachments for the presence of viruses. The >> organization accepts no liability for any damage caused by any virus >> transmitted by this email. >>> ================================= >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> This message was secured via TLS by MUSC. >> |
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Julian Smith III |
Re: seeking "reliable literature" on correct imaging
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Joining the chorus, I would love to have a copy of this powerpoint as well. Best, Julian On 11/21/18 1:56 AM, Julia Edgar wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. > Best wishes > Julia > > > Sent from my iPhone. Please excuse typos. > >> On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> Post images on http://www.imgur.com and include the link in your posting. >> ***** >> >> Mike, >> >> I too would also appreciate this PowerPoint. I think in the context of the >> ethics thread, this is very interesting and useful conversation. My >> students are currently in the mandated ethics class and the topics >> discussed are crazy extremes that really have their roots in 'smaller' less >> obvious mistakes to most people. Focusing the discussion on what they are >> doing in the lab to protect the quality of data or understand limitations >> seems more important to me, than discussing ethics of CRISPR and human >> life. >> >> Karissa >> >> On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor <[hidden email] >> wrote: >> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your posting. >>> ***** >>> >>> Hi >>> I do visit various institutions to teach basics on microscopy and imaging >>> always struggle convey the right message in the absence of a proper >>> material.. >>> Your presentation may be really a good tool for me to convey correct >>> message and make the next generation scientist fool proof.. >>> Kindly provide me the PPT .. >>> Reg >>> Ganesh Kadasoor >>> Bangalore >>> India >>> >>> >>> Sent from my iPhone >>> >>>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> >>> wrote: >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike, >>>> >>>> I would like a copy of the PowerPoint as well. This is a very important >>> issue that Michael Cammer raises. Trainees (and even more senior folks) >>> continue to make these mistakes even as you emphatically tell them not to. >>>> Thanks again, >>>> >>>> John >>>> >>>> -- >>>> John J. Lemasters, MD, PhD >>>> Professor and GlaxoSmithKline Distinguished Endowed Chair >>>> Director, Center for Cell Death, Injury & Regeneration >>>> Departments of Drug Discovery & Biomedical Sciences and Biochemistry & >>> Molecular Biology >>>> Medical University of South Carolina >>>> DD504 Drug Discovery Building >>>> 70 President Street, MSC 139 >>>> Charleston, SC 29425 >>>> >>>> Office: 843-876-2360 >>>> Lab: 843-876-2354 >>>> Fax: 843-876-2353 >>>> Email: [hidden email] >>>> http://academicdepartments.musc.edu/ccdir >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List [mailto:[hidden email]] >>> On Behalf Of Kathryn Spencer >>>> Sent: Friday, November 16, 2018 12:32 PM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> CAUTION: External >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike; >>>> Could I get your PowerPoint as well? I have the same issues with >>> my users. I'm "retraining" all of them with an open-software quiz, to see >>> if they understand basic concepts. Many are complaining and reluctant, >>> because they don't see the issues with their images. This after one 6-year >>> post-doc's data was totally discarded because she saved everything as >>> JPG....I certainly NEVER taught her to do THAT. >>>> Your PowerPoint should hold more credibility that I obviously >>> have.... >>>> Best; >>>> Kathy >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of MODEL, MICHAEL >>>> Sent: Friday, November 16, 2018 9:00 AM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Michael, >>>> >>>> We recently ran a workshop where I gave a 3-hour talk on various kinds >>> of quantification in microscopy. I can send you a PowerPoint file but don't >>> have a text. >>>> Mike Model >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of Cammer, Michael >>>> Sent: Friday, November 16, 2018 11:50 AM >>>> To: [hidden email] >>>> Subject: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Increasingly we have found that microscope users do not understand >>> proper imaging. >>>> A few examples: >>>> Confocal images are saturated and have the offset set to negative >>> numbers intentionally "to reduce background". >>>> Exposures are changed in fluorescent micrographs to make each one "look >>> good". >>>> 16 bit raw data with no saturation or clipping are set to 8 bits with a >>> lot of saturated and clipped pixels at the extremes and these are what are >>> considered raw data. >>>> JPG compression is great because images can be emailed. >>>> People assume (and get angry when this doesn't work) that computers can >>> automatically segment and count anything regardless of experimental design, >>> image quality, etc. >>>> Even if they have saved everything as TIF with no metadata and forgot >>> what magnifications they used. >>>> A student who recognizes these problems and wants to learn the right way >>> emailed me yesterday asking for "any reliable literature you recommend if >>> I'd like to read more about correct imaging." >>>> I did Google searches and, after skimming a bunch of web pages, realized >>> that I didn't really have an answer. I could send to this page and to this >>> page, but it's not a coherent narrative. And I don't have a library; most >>> of what I know about this was picked up willy-nilly up in the 1980s and >>> '90s. For instance knowledge of color separation from writing animations >>> for the Apple II in machine code, working in a cable TV studio in the >>> 1980s, and from an art history class in college where we discussed 19th C >>> travel photos and poly/monochromatic film chemistries of the periods. >>> Later I learned fluorescence quantification from a cell biologist intent on >>> making sure we had true linear responses for readouts of f-actin mass and >>> concentration, I was fortunate to attend both a Woods Hole microscopy >>> course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 >>> training course at their offices in Cambridge, MA covered a lot of material >>> on this too. >>>> So, do people have favorite texts that cover these topics in a manner >>> digestible by new generations of students? Of biology students. Keep in >>> mind many don't know what a byte is; when I teach I ask the class if anyone >>> knows why an image is coded with white as 255 or 4095 or 16383 and >>> typically one or two hands go up but the rest of the class really doesn't >>> know. >>>> Looking forward to suggestions of easy to read definitive texts! >>>> >>>> Thank you. >>>> >>>> Cheers- >>>> >>>> >>>> ------------------------------------------------------------ >>>> This email message, including any attachments, is for the sole use of >>> the intended recipient(s) and may contain information that is proprietary, >>> confidential, and exempt from disclosure under applicable law. Any >>> unauthorized review, use, disclosure, or distribution is prohibited. If you >>> have received this email in error please notify the sender by return email >>> and delete the original message. Please note, the recipient should check >>> this email and any attachments for the presence of viruses. The >>> organization accepts no liability for any damage caused by any virus >>> transmitted by this email. >>>> ================================= >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> This message was secured via TLS by MUSC. -- Julian P.S. Smith III Director, Winthrop Microscopy Facility Dept. of Biology Winthrop University 349 Columbia Ave Rock Hill, SCÊ 29733 803-323-2111 x6427 (vox) 803-323-3448 (fax) 803-524-2347 (cell) Research Website www.birdnest.org/smithj Personal Website www.rociada-east.net |
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Gerhard Holst |
AW: seeking "reliable literature" on correct imaging
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** I would appreciate to reive a copy of that powerpoint too, Mike. with best regards, Gerhard Holst Dr. Gerhard Holst Head of Science & Research +49 (0) 9441 2005 0 +49 (0) 172 711 6049 PCO AG, Donaupark 11, 93309 Kelheim, Germany, www.pco.de USt. ID-Nr. / VAT: DE128590843, Registergericht / Register court: Regensburg HRB 9157 Sitz der Gesellschaft / Registered office: Kelheim, Vorstand / Chairman: Dr. Emil Ott Vorsitzender des Aufsichtsrats / Chairman of the supervisory board: Johann Plöb -----Ursprüngliche Nachricht----- Von: Confocal Microscopy List [mailto:[hidden email]] Im Auftrag von Smith, III, Julian P.S Gesendet: Mittwoch, 21. November 2018 14:48 An: [hidden email] Betreff: [SPAM] Re: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Joining the chorus, I would love to have a copy of this powerpoint as well. Best, Julian On 11/21/18 1:56 AM, Julia Edgar wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. > Best wishes > Julia > > > Sent from my iPhone. Please excuse typos. > >> On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> Post images on http://www.imgur.com and include the link in your posting. >> ***** >> >> Mike, >> >> I too would also appreciate this PowerPoint. I think in the context of the >> ethics thread, this is very interesting and useful conversation. My >> students are currently in the mandated ethics class and the topics >> discussed are crazy extremes that really have their roots in 'smaller' less >> obvious mistakes to most people. Focusing the discussion on what they are >> doing in the lab to protect the quality of data or understand limitations >> seems more important to me, than discussing ethics of CRISPR and human >> life. >> >> Karissa >> >> On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor <[hidden email] >> wrote: >> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your posting. >>> ***** >>> >>> Hi >>> I do visit various institutions to teach basics on microscopy and imaging >>> always struggle convey the right message in the absence of a proper >>> material.. >>> Your presentation may be really a good tool for me to convey correct >>> message and make the next generation scientist fool proof.. >>> Kindly provide me the PPT .. >>> Reg >>> Ganesh Kadasoor >>> Bangalore >>> India >>> >>> >>> Sent from my iPhone >>> >>>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> >>> wrote: >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike, >>>> >>>> I would like a copy of the PowerPoint as well. This is a very important >>> issue that Michael Cammer raises. Trainees (and even more senior folks) >>> continue to make these mistakes even as you emphatically tell them not to. >>>> Thanks again, >>>> >>>> John >>>> >>>> -- >>>> John J. Lemasters, MD, PhD >>>> Professor and GlaxoSmithKline Distinguished Endowed Chair >>>> Director, Center for Cell Death, Injury & Regeneration >>>> Departments of Drug Discovery & Biomedical Sciences and Biochemistry & >>> Molecular Biology >>>> Medical University of South Carolina >>>> DD504 Drug Discovery Building >>>> 70 President Street, MSC 139 >>>> Charleston, SC 29425 >>>> >>>> Office: 843-876-2360 >>>> Lab: 843-876-2354 >>>> Fax: 843-876-2353 >>>> Email: [hidden email] >>>> http://academicdepartments.musc.edu/ccdir >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List [mailto:[hidden email]] >>> On Behalf Of Kathryn Spencer >>>> Sent: Friday, November 16, 2018 12:32 PM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> CAUTION: External >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike; >>>> Could I get your PowerPoint as well? I have the same issues with >>> my users. I'm "retraining" all of them with an open-software quiz, to see >>> if they understand basic concepts. Many are complaining and reluctant, >>> because they don't see the issues with their images. This after one 6-year >>> post-doc's data was totally discarded because she saved everything as >>> JPG....I certainly NEVER taught her to do THAT. >>>> Your PowerPoint should hold more credibility that I obviously >>> have.... >>>> Best; >>>> Kathy >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of MODEL, MICHAEL >>>> Sent: Friday, November 16, 2018 9:00 AM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Michael, >>>> >>>> We recently ran a workshop where I gave a 3-hour talk on various kinds >>> of quantification in microscopy. I can send you a PowerPoint file but don't >>> have a text. >>>> Mike Model >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of Cammer, Michael >>>> Sent: Friday, November 16, 2018 11:50 AM >>>> To: [hidden email] >>>> Subject: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Increasingly we have found that microscope users do not understand >>> proper imaging. >>>> A few examples: >>>> Confocal images are saturated and have the offset set to negative >>> numbers intentionally "to reduce background". >>>> Exposures are changed in fluorescent micrographs to make each one "look >>> good". >>>> 16 bit raw data with no saturation or clipping are set to 8 bits with a >>> lot of saturated and clipped pixels at the extremes and these are what are >>> considered raw data. >>>> JPG compression is great because images can be emailed. >>>> People assume (and get angry when this doesn't work) that computers can >>> automatically segment and count anything regardless of experimental design, >>> image quality, etc. >>>> Even if they have saved everything as TIF with no metadata and forgot >>> what magnifications they used. >>>> A student who recognizes these problems and wants to learn the right way >>> emailed me yesterday asking for "any reliable literature you recommend if >>> I'd like to read more about correct imaging." >>>> I did Google searches and, after skimming a bunch of web pages, realized >>> that I didn't really have an answer. I could send to this page and to this >>> page, but it's not a coherent narrative. And I don't have a library; most >>> of what I know about this was picked up willy-nilly up in the 1980s and >>> '90s. For instance knowledge of color separation from writing animations >>> for the Apple II in machine code, working in a cable TV studio in the >>> 1980s, and from an art history class in college where we discussed 19th C >>> travel photos and poly/monochromatic film chemistries of the periods. >>> Later I learned fluorescence quantification from a cell biologist intent on >>> making sure we had true linear responses for readouts of f-actin mass and >>> concentration, I was fortunate to attend both a Woods Hole microscopy >>> course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 >>> training course at their offices in Cambridge, MA covered a lot of material >>> on this too. >>>> So, do people have favorite texts that cover these topics in a manner >>> digestible by new generations of students? Of biology students. Keep in >>> mind many don't know what a byte is; when I teach I ask the class if anyone >>> knows why an image is coded with white as 255 or 4095 or 16383 and >>> typically one or two hands go up but the rest of the class really doesn't >>> know. >>>> Looking forward to suggestions of easy to read definitive texts! >>>> >>>> Thank you. >>>> >>>> Cheers- >>>> >>>> >>>> ------------------------------------------------------------ >>>> This email message, including any attachments, is for the sole use of >>> the intended recipient(s) and may contain information that is proprietary, >>> confidential, and exempt from disclosure under applicable law. Any >>> unauthorized review, use, disclosure, or distribution is prohibited. If you >>> have received this email in error please notify the sender by return email >>> and delete the original message. Please note, the recipient should check >>> this email and any attachments for the presence of viruses. The >>> organization accepts no liability for any damage caused by any virus >>> transmitted by this email. >>>> ================================= >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> This message was secured via TLS by MUSC. -- Julian P.S. Smith III Director, Winthrop Microscopy Facility Dept. of Biology Winthrop University 349 Columbia Ave Rock Hill, SCÊ 29733 803-323-2111 x6427 (vox) 803-323-3448 (fax) 803-524-2347 (cell) Research Website www.birdnest.org/smithj Personal Website www.rociada-east.net |
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Tanneke den Blaauwen |
Re: seeking "reliable literature" on correct imaging
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In reply to this post by Julian Smith III
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** I am also joning th chorus that would like to have the powerpoint1 Thank you very much, Tanneke den Blaauwen On 21 Nov 2018, at 14:47, Smith, III, Julian P.S <[hidden email]<mailto:[hidden email]>> wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Joining the chorus, I would love to have a copy of this powerpoint as well. Best, Julian On 11/21/18 1:56 AM, Julia Edgar wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. Best wishes Julia Sent from my iPhone. Please excuse typos. On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Mike, I too would also appreciate this PowerPoint. I think in the context of the ethics thread, this is very interesting and useful conversation. My students are currently in the mandated ethics class and the topics discussed are crazy extremes that really have their roots in 'smaller' less obvious mistakes to most people. Focusing the discussion on what they are doing in the lab to protect the quality of data or understand limitations seems more important to me, than discussing ethics of CRISPR and human life. Karissa On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor <[hidden email] wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi I do visit various institutions to teach basics on microscopy and imaging always struggle convey the right message in the absence of a proper material.. Your presentation may be really a good tool for me to convey correct message and make the next generation scientist fool proof.. Kindly provide me the PPT .. Reg Ganesh Kadasoor Bangalore India Sent from my iPhone On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> wrote: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Mike, I would like a copy of the PowerPoint as well. This is a very important issue that Michael Cammer raises. Trainees (and even more senior folks) continue to make these mistakes even as you emphatically tell them not to. Thanks again, John -- John J. Lemasters, MD, PhD Professor and GlaxoSmithKline Distinguished Endowed Chair Director, Center for Cell Death, Injury & Regeneration Departments of Drug Discovery & Biomedical Sciences and Biochemistry & Molecular Biology Medical University of South Carolina DD504 Drug Discovery Building 70 President Street, MSC 139 Charleston, SC 29425 Office: 843-876-2360 Lab: 843-876-2354 Fax: 843-876-2353 Email: [hidden email] http://academicdepartments.musc.edu/ccdir -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Kathryn Spencer Sent: Friday, November 16, 2018 12:32 PM To: [hidden email] Subject: Re: seeking "reliable literature" on correct imaging CAUTION: External ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Mike; Could I get your PowerPoint as well? I have the same issues with my users. I'm "retraining" all of them with an open-software quiz, to see if they understand basic concepts. Many are complaining and reluctant, because they don't see the issues with their images. This after one 6-year post-doc's data was totally discarded because she saved everything as JPG....I certainly NEVER taught her to do THAT. Your PowerPoint should hold more credibility that I obviously have.... Best; Kathy -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of MODEL, MICHAEL Sent: Friday, November 16, 2018 9:00 AM To: [hidden email] Subject: Re: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Michael, We recently ran a workshop where I gave a 3-hour talk on various kinds of quantification in microscopy. I can send you a PowerPoint file but don't have a text. Mike Model -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of Cammer, Michael Sent: Friday, November 16, 2018 11:50 AM To: [hidden email] Subject: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Increasingly we have found that microscope users do not understand proper imaging. A few examples: Confocal images are saturated and have the offset set to negative numbers intentionally "to reduce background". Exposures are changed in fluorescent micrographs to make each one "look good". 16 bit raw data with no saturation or clipping are set to 8 bits with a lot of saturated and clipped pixels at the extremes and these are what are considered raw data. JPG compression is great because images can be emailed. People assume (and get angry when this doesn't work) that computers can automatically segment and count anything regardless of experimental design, image quality, etc. Even if they have saved everything as TIF with no metadata and forgot what magnifications they used. A student who recognizes these problems and wants to learn the right way emailed me yesterday asking for "any reliable literature you recommend if I'd like to read more about correct imaging." I did Google searches and, after skimming a bunch of web pages, realized that I didn't really have an answer. I could send to this page and to this page, but it's not a coherent narrative. And I don't have a library; most of what I know about this was picked up willy-nilly up in the 1980s and '90s. For instance knowledge of color separation from writing animations for the Apple II in machine code, working in a cable TV studio in the 1980s, and from an art history class in college where we discussed 19th C travel photos and poly/monochromatic film chemistries of the periods. Later I learned fluorescence quantification from a cell biologist intent on making sure we had true linear responses for readouts of f-actin mass and concentration, I was fortunate to attend both a Woods Hole microscopy course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 training course at their offices in Cambridge, MA covered a lot of material on this too. So, do people have favorite texts that cover these topics in a manner digestible by new generations of students? Of biology students. Keep in mind many don't know what a byte is; when I teach I ask the class if anyone knows why an image is coded with white as 255 or 4095 or 16383 and typically one or two hands go up but the rest of the class really doesn't know. Looking forward to suggestions of easy to read definitive texts! Thank you. Cheers- ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ------------------------------------------------------------------------- This message was secured via TLS by MUSC. -- Julian P.S. Smith III Director, Winthrop Microscopy Facility Dept. of Biology Winthrop University 349 Columbia Ave Rock Hill, SCÊ 29733 803-323-2111 x6427 (vox) 803-323-3448 (fax) 803-524-2347 (cell) Research Website www.birdnest.org/smithj Personal Website www.rociada-east.net Tanneke den Blaauwen Assoc prof Bacterial Cell Biology SILS, UvA Science Park 904, C3.108 1098 XH Amsterdam, NL [hidden email]<mailto:[hidden email]> |
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In reply to this post by Gerhard Holst
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear colleagues, Here is the link to the file https://www.dropbox.com/s/cgnx2r1pk3v5oon/Quantitative%20Biological%20Microscopy.pptx?dl=0 All the best Mike -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of Gerhard Holst Sent: Wednesday, November 21, 2018 9:02 AM To: [hidden email] Subject: AW: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** I would appreciate to reive a copy of that powerpoint too, Mike. with best regards, Gerhard Holst Dr. Gerhard Holst Head of Science & Research +49 (0) 9441 2005 0 +49 (0) 172 711 6049 PCO AG, Donaupark 11, 93309 Kelheim, Germany, www.pco.de USt. ID-Nr. / VAT: DE128590843, Registergericht / Register court: Regensburg HRB 9157 Sitz der Gesellschaft / Registered office: Kelheim, Vorstand / Chairman: Dr. Emil Ott Vorsitzender des Aufsichtsrats / Chairman of the supervisory board: Johann Plöb -----Ursprüngliche Nachricht----- Von: Confocal Microscopy List [mailto:[hidden email]] Im Auftrag von Smith, III, Julian P.S Gesendet: Mittwoch, 21. November 2018 14:48 An: [hidden email] Betreff: [SPAM] Re: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Joining the chorus, I would love to have a copy of this powerpoint as well. Best, Julian On 11/21/18 1:56 AM, Julia Edgar wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. > Best wishes > Julia > > > Sent from my iPhone. Please excuse typos. > >> On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> Post images on http://www.imgur.com and include the link in your posting. >> ***** >> >> Mike, >> >> I too would also appreciate this PowerPoint. I think in the context >> of the ethics thread, this is very interesting and useful >> conversation. My students are currently in the mandated ethics class >> and the topics discussed are crazy extremes that really have their >> roots in 'smaller' less obvious mistakes to most people. Focusing the >> discussion on what they are doing in the lab to protect the quality >> of data or understand limitations seems more important to me, than >> discussing ethics of CRISPR and human life. >> >> Karissa >> >> On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor >> <[hidden email] >> wrote: >> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your posting. >>> ***** >>> >>> Hi >>> I do visit various institutions to teach basics on microscopy and >>> imaging always struggle convey the right message in the absence of a >>> proper material.. >>> Your presentation may be really a good tool for me to convey correct >>> message and make the next generation scientist fool proof.. >>> Kindly provide me the PPT .. >>> Reg >>> Ganesh Kadasoor >>> Bangalore >>> India >>> >>> >>> Sent from my iPhone >>> >>>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> >>> wrote: >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike, >>>> >>>> I would like a copy of the PowerPoint as well. This is a very >>>> important >>> issue that Michael Cammer raises. Trainees (and even more senior >>> folks) continue to make these mistakes even as you emphatically tell them not to. >>>> Thanks again, >>>> >>>> John >>>> >>>> -- >>>> John J. Lemasters, MD, PhD >>>> Professor and GlaxoSmithKline Distinguished Endowed Chair Director, >>>> Center for Cell Death, Injury & Regeneration Departments of Drug >>>> Discovery & Biomedical Sciences and Biochemistry & >>> Molecular Biology >>>> Medical University of South Carolina >>>> DD504 Drug Discovery Building >>>> 70 President Street, MSC 139 >>>> Charleston, SC 29425 >>>> >>>> Office: 843-876-2360 >>>> Lab: 843-876-2354 >>>> Fax: 843-876-2353 >>>> Email: [hidden email] >>>> http://academicdepartments.musc.edu/ccdir >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List >>>> [mailto:[hidden email]] >>> On Behalf Of Kathryn Spencer >>>> Sent: Friday, November 16, 2018 12:32 PM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> CAUTION: External >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike; >>>> Could I get your PowerPoint as well? I have the same issues >>>> with >>> my users. I'm "retraining" all of them with an open-software quiz, >>> to see if they understand basic concepts. Many are complaining and >>> reluctant, because they don't see the issues with their images. This >>> after one 6-year post-doc's data was totally discarded because she >>> saved everything as JPG....I certainly NEVER taught her to do THAT. >>>> Your PowerPoint should hold more credibility that I >>>> obviously >>> have.... >>>> Best; >>>> Kathy >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> >>>> On >>> Behalf Of MODEL, MICHAEL >>>> Sent: Friday, November 16, 2018 9:00 AM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Michael, >>>> >>>> We recently ran a workshop where I gave a 3-hour talk on various >>>> kinds >>> of quantification in microscopy. I can send you a PowerPoint file >>> but don't have a text. >>>> Mike Model >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> >>>> On >>> Behalf Of Cammer, Michael >>>> Sent: Friday, November 16, 2018 11:50 AM >>>> To: [hidden email] >>>> Subject: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Increasingly we have found that microscope users do not understand >>> proper imaging. >>>> A few examples: >>>> Confocal images are saturated and have the offset set to negative >>> numbers intentionally "to reduce background". >>>> Exposures are changed in fluorescent micrographs to make each one >>>> "look >>> good". >>>> 16 bit raw data with no saturation or clipping are set to 8 bits >>>> with a >>> lot of saturated and clipped pixels at the extremes and these are >>> what are considered raw data. >>>> JPG compression is great because images can be emailed. >>>> People assume (and get angry when this doesn't work) that computers >>>> can >>> automatically segment and count anything regardless of experimental >>> design, image quality, etc. >>>> Even if they have saved everything as TIF with no metadata and >>>> forgot >>> what magnifications they used. >>>> A student who recognizes these problems and wants to learn the >>>> right way >>> emailed me yesterday asking for "any reliable literature you >>> recommend if I'd like to read more about correct imaging." >>>> I did Google searches and, after skimming a bunch of web pages, >>>> realized >>> that I didn't really have an answer. I could send to this page and >>> to this page, but it's not a coherent narrative. And I don't have a >>> library; most of what I know about this was picked up willy-nilly up >>> in the 1980s and '90s. For instance knowledge of color separation >>> from writing animations for the Apple II in machine code, working in >>> a cable TV studio in the 1980s, and from an art history class in >>> college where we discussed 19th C travel photos and poly/monochromatic film chemistries of the periods. >>> Later I learned fluorescence quantification from a cell biologist >>> intent on making sure we had true linear responses for readouts of >>> f-actin mass and concentration, I was fortunate to attend both a >>> Woods Hole microscopy course and at NCSU John Russ's course on image >>> analysis, and BioRad MRC 600 training course at their offices in >>> Cambridge, MA covered a lot of material on this too. >>>> So, do people have favorite texts that cover these topics in a >>>> manner >>> digestible by new generations of students? Of biology students. >>> Keep in mind many don't know what a byte is; when I teach I ask the >>> class if anyone knows why an image is coded with white as 255 or >>> 4095 or 16383 and typically one or two hands go up but the rest of >>> the class really doesn't know. >>>> Looking forward to suggestions of easy to read definitive texts! >>>> >>>> Thank you. >>>> >>>> Cheers- >>>> >>>> >>>> ------------------------------------------------------------ >>>> This email message, including any attachments, is for the sole use >>>> of >>> the intended recipient(s) and may contain information that is >>> proprietary, confidential, and exempt from disclosure under >>> applicable law. Any unauthorized review, use, disclosure, or >>> distribution is prohibited. If you have received this email in error >>> please notify the sender by return email and delete the original >>> message. Please note, the recipient should check this email and any >>> attachments for the presence of viruses. The organization accepts no >>> liability for any damage caused by any virus transmitted by this email. >>>> ================================= >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> ------ This message was secured via TLS by MUSC. -- Julian P.S. Smith III Director, Winthrop Microscopy Facility Dept. of Biology Winthrop University 349 Columbia Ave Rock Hill, SCÊ 29733 803-323-2111 x6427 (vox) 803-323-3448 (fax) 803-524-2347 (cell) Research Website www.birdnest.org/smithj Personal Website www.rociada-east.net |
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Martin Wessendorf-2 |
Re: seeking "reliable literature" on correct imaging
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Thank you, Mike! You generosity is appreciated! Martin Wessendorf On 11/21/2018 9:22 AM, MODEL, MICHAEL wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Dear colleagues, > Here is the link to the file > > https://www.dropbox.com/s/cgnx2r1pk3v5oon/Quantitative%20Biological%20Microscopy.pptx?dl=0 > > All the best > > Mike > > > -----Original Message----- > From: Confocal Microscopy List <[hidden email]> On Behalf Of Gerhard Holst > Sent: Wednesday, November 21, 2018 9:02 AM > To: [hidden email] > Subject: AW: seeking "reliable literature" on correct imaging > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > I would appreciate to reive a copy of that powerpoint too, Mike. > > with best regards, > > Gerhard Holst > > > Dr. Gerhard Holst > Head of Science & Research > +49 (0) 9441 2005 0 > +49 (0) 172 711 6049 > > PCO AG, Donaupark 11, 93309 Kelheim, Germany, www.pco.de USt. ID-Nr. / VAT: DE128590843, Registergericht / Register court: Regensburg HRB 9157 Sitz der Gesellschaft / Registered office: Kelheim, Vorstand / Chairman: Dr. Emil Ott Vorsitzender des Aufsichtsrats / Chairman of the supervisory board: Johann Plöb > > -----Ursprüngliche Nachricht----- > Von: Confocal Microscopy List [mailto:[hidden email]] Im Auftrag von Smith, III, Julian P.S > Gesendet: Mittwoch, 21. November 2018 14:48 > An: [hidden email] > Betreff: [SPAM] Re: seeking "reliable literature" on correct imaging > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Joining the chorus, I would love to have a copy of this powerpoint as well. > Best, > Julian > > On 11/21/18 1:56 AM, Julia Edgar wrote: >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> Post images on http://www.imgur.com and include the link in your posting. >> ***** >> >> Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. >> Best wishes >> Julia >> >> >> Sent from my iPhone. Please excuse typos. >> >>> On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: >>> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your posting. >>> ***** >>> >>> Mike, >>> >>> I too would also appreciate this PowerPoint. I think in the context >>> of the ethics thread, this is very interesting and useful >>> conversation. My students are currently in the mandated ethics class >>> and the topics discussed are crazy extremes that really have their >>> roots in 'smaller' less obvious mistakes to most people. Focusing the >>> discussion on what they are doing in the lab to protect the quality >>> of data or understand limitations seems more important to me, than >>> discussing ethics of CRISPR and human life. >>> >>> Karissa >>> >>> On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor >>> <[hidden email] >>> wrote: >>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your posting. >>>> ***** >>>> >>>> Hi >>>> I do visit various institutions to teach basics on microscopy and >>>> imaging always struggle convey the right message in the absence of a >>>> proper material.. >>>> Your presentation may be really a good tool for me to convey correct >>>> message and make the next generation scientist fool proof.. >>>> Kindly provide me the PPT .. >>>> Reg >>>> Ganesh Kadasoor >>>> Bangalore >>>> India >>>> >>>> >>>> Sent from my iPhone >>>> >>>>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> >>>> wrote: >>>>> ***** >>>>> To join, leave or search the confocal microscopy listserv, go to: >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>>> Post images on http://www.imgur.com and include the link in your >>>> posting. >>>>> ***** >>>>> >>>>> Hi Mike, >>>>> >>>>> I would like a copy of the PowerPoint as well. This is a very >>>>> important >>>> issue that Michael Cammer raises. Trainees (and even more senior >>>> folks) continue to make these mistakes even as you emphatically tell them not to. >>>>> Thanks again, >>>>> >>>>> John >>>>> >>>>> -- >>>>> John J. Lemasters, MD, PhD >>>>> Professor and GlaxoSmithKline Distinguished Endowed Chair Director, >>>>> Center for Cell Death, Injury & Regeneration Departments of Drug >>>>> Discovery & Biomedical Sciences and Biochemistry & >>>> Molecular Biology >>>>> Medical University of South Carolina >>>>> DD504 Drug Discovery Building >>>>> 70 President Street, MSC 139 >>>>> Charleston, SC 29425 >>>>> >>>>> Office: 843-876-2360 >>>>> Lab: 843-876-2354 >>>>> Fax: 843-876-2353 >>>>> Email: [hidden email] >>>>> http://academicdepartments.musc.edu/ccdir >>>>> >>>>> -----Original Message----- >>>>> From: Confocal Microscopy List >>>>> [mailto:[hidden email]] >>>> On Behalf Of Kathryn Spencer >>>>> Sent: Friday, November 16, 2018 12:32 PM >>>>> To: [hidden email] >>>>> Subject: Re: seeking "reliable literature" on correct imaging >>>>> >>>>> CAUTION: External >>>>> >>>>> ***** >>>>> To join, leave or search the confocal microscopy listserv, go to: >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>>> Post images on http://www.imgur.com and include the link in your >>>> posting. >>>>> ***** >>>>> >>>>> Hi Mike; >>>>> Could I get your PowerPoint as well? I have the same issues >>>>> with >>>> my users. I'm "retraining" all of them with an open-software quiz, >>>> to see if they understand basic concepts. Many are complaining and >>>> reluctant, because they don't see the issues with their images. This >>>> after one 6-year post-doc's data was totally discarded because she >>>> saved everything as JPG....I certainly NEVER taught her to do THAT. >>>>> Your PowerPoint should hold more credibility that I >>>>> obviously >>>> have.... >>>>> Best; >>>>> Kathy >>>>> >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Confocal Microscopy List <[hidden email]> >>>>> On >>>> Behalf Of MODEL, MICHAEL >>>>> Sent: Friday, November 16, 2018 9:00 AM >>>>> To: [hidden email] >>>>> Subject: Re: seeking "reliable literature" on correct imaging >>>>> >>>>> ***** >>>>> To join, leave or search the confocal microscopy listserv, go to: >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>>> Post images on http://www.imgur.com and include the link in your >>>> posting. >>>>> ***** >>>>> >>>>> Hi Michael, >>>>> >>>>> We recently ran a workshop where I gave a 3-hour talk on various >>>>> kinds >>>> of quantification in microscopy. I can send you a PowerPoint file >>>> but don't have a text. >>>>> Mike Model >>>>> >>>>> -----Original Message----- >>>>> From: Confocal Microscopy List <[hidden email]> >>>>> On >>>> Behalf Of Cammer, Michael >>>>> Sent: Friday, November 16, 2018 11:50 AM >>>>> To: [hidden email] >>>>> Subject: seeking "reliable literature" on correct imaging >>>>> >>>>> ***** >>>>> To join, leave or search the confocal microscopy listserv, go to: >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>>> Post images on http://www.imgur.com and include the link in your >>>> posting. >>>>> ***** >>>>> >>>>> Increasingly we have found that microscope users do not understand >>>> proper imaging. >>>>> A few examples: >>>>> Confocal images are saturated and have the offset set to negative >>>> numbers intentionally "to reduce background". >>>>> Exposures are changed in fluorescent micrographs to make each one >>>>> "look >>>> good". >>>>> 16 bit raw data with no saturation or clipping are set to 8 bits >>>>> with a >>>> lot of saturated and clipped pixels at the extremes and these are >>>> what are considered raw data. >>>>> JPG compression is great because images can be emailed. >>>>> People assume (and get angry when this doesn't work) that computers >>>>> can >>>> automatically segment and count anything regardless of experimental >>>> design, image quality, etc. >>>>> Even if they have saved everything as TIF with no metadata and >>>>> forgot >>>> what magnifications they used. >>>>> A student who recognizes these problems and wants to learn the >>>>> right way >>>> emailed me yesterday asking for "any reliable literature you >>>> recommend if I'd like to read more about correct imaging." >>>>> I did Google searches and, after skimming a bunch of web pages, >>>>> realized >>>> that I didn't really have an answer. I could send to this page and >>>> to this page, but it's not a coherent narrative. And I don't have a >>>> library; most of what I know about this was picked up willy-nilly up >>>> in the 1980s and '90s. For instance knowledge of color separation >>>> from writing animations for the Apple II in machine code, working in >>>> a cable TV studio in the 1980s, and from an art history class in >>>> college where we discussed 19th C travel photos and poly/monochromatic film chemistries of the periods. >>>> Later I learned fluorescence quantification from a cell biologist >>>> intent on making sure we had true linear responses for readouts of >>>> f-actin mass and concentration, I was fortunate to attend both a >>>> Woods Hole microscopy course and at NCSU John Russ's course on image >>>> analysis, and BioRad MRC 600 training course at their offices in >>>> Cambridge, MA covered a lot of material on this too. >>>>> So, do people have favorite texts that cover these topics in a >>>>> manner >>>> digestible by new generations of students? Of biology students. >>>> Keep in mind many don't know what a byte is; when I teach I ask the >>>> class if anyone knows why an image is coded with white as 255 or >>>> 4095 or 16383 and typically one or two hands go up but the rest of >>>> the class really doesn't know. >>>>> Looking forward to suggestions of easy to read definitive texts! >>>>> >>>>> Thank you. >>>>> >>>>> Cheers- >>>>> >>>>> >>>>> ------------------------------------------------------------ >>>>> This email message, including any attachments, is for the sole use >>>>> of >>>> the intended recipient(s) and may contain information that is >>>> proprietary, confidential, and exempt from disclosure under >>>> applicable law. Any unauthorized review, use, disclosure, or >>>> distribution is prohibited. If you have received this email in error >>>> please notify the sender by return email and delete the original >>>> message. Please note, the recipient should check this email and any >>>> attachments for the presence of viruses. The organization accepts no >>>> liability for any damage caused by any virus transmitted by this email. >>>>> ================================= >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------- >>>>> ------ This message was secured via TLS by MUSC. > > -- > Julian P.S. Smith III > Director, Winthrop Microscopy Facility > Dept. of Biology > Winthrop University > 349 Columbia Ave > Rock Hill, SCÊ 29733 > > 803-323-2111 x6427 (vox) > 803-323-3448 (fax) > 803-524-2347 (cell) > Research Website www.birdnest.org/smithj Personal Website www.rociada-east.net > -- Martin Wessendorf, Ph.D. office: (612) 626-0145 Assoc Prof, Dept Neuroscience lab: (612) 624-2991 University of Minnesota Preferred FAX: (612) 624-8118 6-145 Jackson Hall, 321 Church St. SE Dept Fax: (612) 626-5009 Minneapolis, MN 55455 e-mail: [hidden email] |
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Craig Brideau |
Re: seeking "reliable literature" on correct imaging
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Thanks! Looking forward to reading it. Craig On Wed, Nov 21, 2018 at 9:33 AM Martin Wessendorf <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Thank you, Mike! You generosity is appreciated! > > Martin Wessendorf > > > > > On 11/21/2018 9:22 AM, MODEL, MICHAEL wrote: > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > Post images on http://www.imgur.com and include the link in your > posting. > > ***** > > > > Dear colleagues, > > Here is the link to the file > > > > > https://www.dropbox.com/s/cgnx2r1pk3v5oon/Quantitative%20Biological%20Microscopy.pptx?dl=0 > > > > All the best > > > > Mike > > > > > > -----Original Message----- > > From: Confocal Microscopy List <[hidden email]> On > Behalf Of Gerhard Holst > > Sent: Wednesday, November 21, 2018 9:02 AM > > To: [hidden email] > > Subject: AW: seeking "reliable literature" on correct imaging > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > Post images on http://www.imgur.com and include the link in your > posting. > > ***** > > > > I would appreciate to reive a copy of that powerpoint too, Mike. > > > > with best regards, > > > > Gerhard Holst > > > > > > Dr. Gerhard Holst > > Head of Science & Research > > +49 (0) 9441 2005 0 > > +49 (0) 172 711 6049 > > > > PCO AG, Donaupark 11, 93309 Kelheim, Germany, www.pco.de USt. ID-Nr. / > VAT: DE128590843, Registergericht / Register court: Regensburg HRB 9157 > Sitz der Gesellschaft / Registered office: Kelheim, Vorstand / Chairman: > Dr. Emil Ott Vorsitzender des Aufsichtsrats / Chairman of the supervisory > board: Johann Plöb > > > > -----Ursprüngliche Nachricht----- > > Von: Confocal Microscopy List [mailto:[hidden email]] > Im Auftrag von Smith, III, Julian P.S > > Gesendet: Mittwoch, 21. November 2018 14:48 > > An: [hidden email] > > Betreff: [SPAM] Re: seeking "reliable literature" on correct imaging > > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > > Post images on http://www.imgur.com and include the link in your > posting. > > ***** > > > > Joining the chorus, I would love to have a copy of this powerpoint as > well. > > Best, > > Julian > > > > On 11/21/18 1:56 AM, Julia Edgar wrote: > >> ***** > >> To join, leave or search the confocal microscopy listserv, go to: > >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >> Post images on http://www.imgur.com and include the link in your > posting. > >> ***** > >> > >> Would love to have it too, if possible. I hope your name is pasted all > over it so you get due credit. > >> Best wishes > >> Julia > >> > >> > >> Sent from my iPhone. Please excuse typos. > >> > >>> On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> > wrote: > >>> > >>> ***** > >>> To join, leave or search the confocal microscopy listserv, go to: > >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >>> Post images on http://www.imgur.com and include the link in your > posting. > >>> ***** > >>> > >>> Mike, > >>> > >>> I too would also appreciate this PowerPoint. I think in the context > >>> of the ethics thread, this is very interesting and useful > >>> conversation. My students are currently in the mandated ethics class > >>> and the topics discussed are crazy extremes that really have their > >>> roots in 'smaller' less obvious mistakes to most people. Focusing the > >>> discussion on what they are doing in the lab to protect the quality > >>> of data or understand limitations seems more important to me, than > >>> discussing ethics of CRISPR and human life. > >>> > >>> Karissa > >>> > >>> On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor > >>> <[hidden email] > >>> wrote: > >>> > >>>> ***** > >>>> To join, leave or search the confocal microscopy listserv, go to: > >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >>>> Post images on http://www.imgur.com and include the link in your > posting. > >>>> ***** > >>>> > >>>> Hi > >>>> I do visit various institutions to teach basics on microscopy and > >>>> imaging always struggle convey the right message in the absence of a > >>>> proper material.. > >>>> Your presentation may be really a good tool for me to convey correct > >>>> message and make the next generation scientist fool proof.. > >>>> Kindly provide me the PPT .. > >>>> Reg > >>>> Ganesh Kadasoor > >>>> Bangalore > >>>> India > >>>> > >>>> > >>>> Sent from my iPhone > >>>> > >>>>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> > >>>> wrote: > >>>>> ***** > >>>>> To join, leave or search the confocal microscopy listserv, go to: > >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >>>>> Post images on http://www.imgur.com and include the link in your > >>>> posting. > >>>>> ***** > >>>>> > >>>>> Hi Mike, > >>>>> > >>>>> I would like a copy of the PowerPoint as well. This is a very > >>>>> important > >>>> issue that Michael Cammer raises. Trainees (and even more senior > >>>> folks) continue to make these mistakes even as you emphatically tell > them not to. > >>>>> Thanks again, > >>>>> > >>>>> John > >>>>> > >>>>> -- > >>>>> John J. Lemasters, MD, PhD > >>>>> Professor and GlaxoSmithKline Distinguished Endowed Chair Director, > >>>>> Center for Cell Death, Injury & Regeneration Departments of Drug > >>>>> Discovery & Biomedical Sciences and Biochemistry & > >>>> Molecular Biology > >>>>> Medical University of South Carolina > >>>>> DD504 Drug Discovery Building > >>>>> 70 President Street, MSC 139 > >>>>> Charleston, SC 29425 > >>>>> > >>>>> Office: 843-876-2360 > >>>>> Lab: 843-876-2354 > >>>>> Fax: 843-876-2353 > >>>>> Email: [hidden email] > >>>>> http://academicdepartments.musc.edu/ccdir > >>>>> > >>>>> -----Original Message----- > >>>>> From: Confocal Microscopy List > >>>>> [mailto:[hidden email]] > >>>> On Behalf Of Kathryn Spencer > >>>>> Sent: Friday, November 16, 2018 12:32 PM > >>>>> To: [hidden email] > >>>>> Subject: Re: seeking "reliable literature" on correct imaging > >>>>> > >>>>> CAUTION: External > >>>>> > >>>>> ***** > >>>>> To join, leave or search the confocal microscopy listserv, go to: > >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >>>>> Post images on http://www.imgur.com and include the link in your > >>>> posting. > >>>>> ***** > >>>>> > >>>>> Hi Mike; > >>>>> Could I get your PowerPoint as well? I have the same issues > >>>>> with > >>>> my users. I'm "retraining" all of them with an open-software quiz, > >>>> to see if they understand basic concepts. Many are complaining and > >>>> reluctant, because they don't see the issues with their images. This > >>>> after one 6-year post-doc's data was totally discarded because she > >>>> saved everything as JPG....I certainly NEVER taught her to do THAT. > >>>>> Your PowerPoint should hold more credibility that I > >>>>> obviously > >>>> have.... > >>>>> Best; > >>>>> Kathy > >>>>> > >>>>> > >>>>> > >>>>> -----Original Message----- > >>>>> From: Confocal Microscopy List <[hidden email]> > >>>>> On > >>>> Behalf Of MODEL, MICHAEL > >>>>> Sent: Friday, November 16, 2018 9:00 AM > >>>>> To: [hidden email] > >>>>> Subject: Re: seeking "reliable literature" on correct imaging > >>>>> > >>>>> ***** > >>>>> To join, leave or search the confocal microscopy listserv, go to: > >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >>>>> Post images on http://www.imgur.com and include the link in your > >>>> posting. > >>>>> ***** > >>>>> > >>>>> Hi Michael, > >>>>> > >>>>> We recently ran a workshop where I gave a 3-hour talk on various > >>>>> kinds > >>>> of quantification in microscopy. I can send you a PowerPoint file > >>>> but don't have a text. > >>>>> Mike Model > >>>>> > >>>>> -----Original Message----- > >>>>> From: Confocal Microscopy List <[hidden email]> > >>>>> On > >>>> Behalf Of Cammer, Michael > >>>>> Sent: Friday, November 16, 2018 11:50 AM > >>>>> To: [hidden email] > >>>>> Subject: seeking "reliable literature" on correct imaging > >>>>> > >>>>> ***** > >>>>> To join, leave or search the confocal microscopy listserv, go to: > >>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > >>>>> Post images on http://www.imgur.com and include the link in your > >>>> posting. > >>>>> ***** > >>>>> > >>>>> Increasingly we have found that microscope users do not understand > >>>> proper imaging. > >>>>> A few examples: > >>>>> Confocal images are saturated and have the offset set to negative > >>>> numbers intentionally "to reduce background". > >>>>> Exposures are changed in fluorescent micrographs to make each one > >>>>> "look > >>>> good". > >>>>> 16 bit raw data with no saturation or clipping are set to 8 bits > >>>>> with a > >>>> lot of saturated and clipped pixels at the extremes and these are > >>>> what are considered raw data. > >>>>> JPG compression is great because images can be emailed. > >>>>> People assume (and get angry when this doesn't work) that computers > >>>>> can > >>>> automatically segment and count anything regardless of experimental > >>>> design, image quality, etc. > >>>>> Even if they have saved everything as TIF with no metadata and > >>>>> forgot > >>>> what magnifications they used. > >>>>> A student who recognizes these problems and wants to learn the > >>>>> right way > >>>> emailed me yesterday asking for "any reliable literature you > >>>> recommend if I'd like to read more about correct imaging." > >>>>> I did Google searches and, after skimming a bunch of web pages, > >>>>> realized > >>>> that I didn't really have an answer. I could send to this page and > >>>> to this page, but it's not a coherent narrative. And I don't have a > >>>> library; most of what I know about this was picked up willy-nilly up > >>>> in the 1980s and '90s. For instance knowledge of color separation > >>>> from writing animations for the Apple II in machine code, working in > >>>> a cable TV studio in the 1980s, and from an art history class in > >>>> college where we discussed 19th C travel photos and > poly/monochromatic film chemistries of the periods. > >>>> Later I learned fluorescence quantification from a cell biologist > >>>> intent on making sure we had true linear responses for readouts of > >>>> f-actin mass and concentration, I was fortunate to attend both a > >>>> Woods Hole microscopy course and at NCSU John Russ's course on image > >>>> analysis, and BioRad MRC 600 training course at their offices in > >>>> Cambridge, MA covered a lot of material on this too. > >>>>> So, do people have favorite texts that cover these topics in a > >>>>> manner > >>>> digestible by new generations of students? Of biology students. > >>>> Keep in mind many don't know what a byte is; when I teach I ask the > >>>> class if anyone knows why an image is coded with white as 255 or > >>>> 4095 or 16383 and typically one or two hands go up but the rest of > >>>> the class really doesn't know. > >>>>> Looking forward to suggestions of easy to read definitive texts! > >>>>> > >>>>> Thank you. > >>>>> > >>>>> Cheers- > >>>>> > >>>>> > >>>>> ------------------------------------------------------------ > >>>>> This email message, including any attachments, is for the sole use > >>>>> of > >>>> the intended recipient(s) and may contain information that is > >>>> proprietary, confidential, and exempt from disclosure under > >>>> applicable law. Any unauthorized review, use, disclosure, or > >>>> distribution is prohibited. If you have received this email in error > >>>> please notify the sender by return email and delete the original > >>>> message. Please note, the recipient should check this email and any > >>>> attachments for the presence of viruses. The organization accepts no > >>>> liability for any damage caused by any virus transmitted by this > email. > >>>>> ================================= > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ------------------------------------------------------------------- > >>>>> ------ This message was secured via TLS by MUSC. > > > > -- > > Julian P.S. Smith III > > Director, Winthrop Microscopy Facility > > Dept. of Biology > > Winthrop University > > 349 Columbia Ave > > Rock Hill, SCÊ 29733 > > > > 803-323-2111 x6427 (vox) > > 803-323-3448 (fax) > > 803-524-2347 (cell) > > Research Website www.birdnest.org/smithj Personal Website > www.rociada-east.net > > > > -- > Martin Wessendorf, Ph.D. office: (612) 626-0145 > Assoc Prof, Dept Neuroscience lab: (612) 624-2991 > University of Minnesota Preferred FAX: (612) 624-8118 > 6-145 Jackson Hall, 321 Church St. SE Dept Fax: (612) 626-5009 > Minneapolis, MN 55455 e-mail: [hidden email] > |
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In reply to this post by Julian Smith III
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear Mike, I would also like to have this presentation to improve trainings. Thank you, Herlinde -------- Oorspronkelijk bericht -------- Onderwerp: Re: seeking "reliable literature" on correct imaging Van: "Smith, III, Julian P.S" Aan: [hidden email] Cc: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Joining the chorus, I would love to have a copy of this powerpoint as well. Best, Julian On 11/21/18 1:56 AM, Julia Edgar wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. > Best wishes > Julia > > > Sent from my iPhone. Please excuse typos. > >> On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> Post images on http://www.imgur.com and include the link in your posting. >> ***** >> >> Mike, >> >> I too would also appreciate this PowerPoint. I think in the context of the >> ethics thread, this is very interesting and useful conversation. My >> students are currently in the mandated ethics class and the topics >> discussed are crazy extremes that really have their roots in 'smaller' less >> obvious mistakes to most people. Focusing the discussion on what they are >> doing in the lab to protect the quality of data or understand limitations >> seems more important to me, than discussing ethics of CRISPR and human >> life. >> >> Karissa >> >> On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor <[hidden email] >> wrote: >> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your posting. >>> ***** >>> >>> Hi >>> I do visit various institutions to teach basics on microscopy and imaging >>> always struggle convey the right message in the absence of a proper >>> material.. >>> Your presentation may be really a good tool for me to convey correct >>> message and make the next generation scientist fool proof.. >>> Kindly provide me the PPT .. >>> Reg >>> Ganesh Kadasoor >>> Bangalore >>> India >>> >>> >>> Sent from my iPhone >>> >>>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> >>> wrote: >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike, >>>> >>>> I would like a copy of the PowerPoint as well. This is a very important >>> issue that Michael Cammer raises. Trainees (and even more senior folks) >>> continue to make these mistakes even as you emphatically tell them not to. >>>> Thanks again, >>>> >>>> John >>>> >>>> -- >>>> John J. Lemasters, MD, PhD >>>> Professor and GlaxoSmithKline Distinguished Endowed Chair >>>> Director, Center for Cell Death, Injury & Regeneration >>>> Departments of Drug Discovery & Biomedical Sciences and Biochemistry & >>> Molecular Biology >>>> Medical University of South Carolina >>>> DD504 Drug Discovery Building >>>> 70 President Street, MSC 139 >>>> Charleston, SC 29425 >>>> >>>> Office: 843-876-2360 >>>> Lab: 843-876-2354 >>>> Fax: 843-876-2353 >>>> Email: [hidden email] >>>> http://academicdepartments.musc.edu/ccdir >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List [mailto:[hidden email]] >>> On Behalf Of Kathryn Spencer >>>> Sent: Friday, November 16, 2018 12:32 PM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> CAUTION: External >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike; >>>> Could I get your PowerPoint as well? I have the same issues with >>> my users. I'm "retraining" all of them with an open-software quiz, to see >>> if they understand basic concepts. Many are complaining and reluctant, >>> because they don't see the issues with their images. This after one 6-year >>> post-doc's data was totally discarded because she saved everything as >>> JPG....I certainly NEVER taught her to do THAT. >>>> Your PowerPoint should hold more credibility that I obviously >>> have.... >>>> Best; >>>> Kathy >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of MODEL, MICHAEL >>>> Sent: Friday, November 16, 2018 9:00 AM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Michael, >>>> >>>> We recently ran a workshop where I gave a 3-hour talk on various kinds >>> of quantification in microscopy. I can send you a PowerPoint file but don't >>> have a text. >>>> Mike Model >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of Cammer, Michael >>>> Sent: Friday, November 16, 2018 11:50 AM >>>> To: [hidden email] >>>> Subject: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Increasingly we have found that microscope users do not understand >>> proper imaging. >>>> A few examples: >>>> Confocal images are saturated and have the offset set to negative >>> numbers intentionally "to reduce background". >>>> Exposures are changed in fluorescent micrographs to make each one "look >>> good". >>>> 16 bit raw data with no saturation or clipping are set to 8 bits with a >>> lot of saturated and clipped pixels at the extremes and these are what are >>> considered raw data. >>>> JPG compression is great because images can be emailed. >>>> People assume (and get angry when this doesn't work) that computers can >>> automatically segment and count anything regardless of experimental design, >>> image quality, etc. >>>> Even if they have saved everything as TIF with no metadata and forgot >>> what magnifications they used. >>>> A student who recognizes these problems and wants to learn the right way >>> emailed me yesterday asking for "any reliable literature you recommend if >>> I'd like to read more about correct imaging." >>>> I did Google searches and, after skimming a bunch of web pages, realized >>> that I didn't really have an answer. I could send to this page and to this >>> page, but it's not a coherent narrative. And I don't have a library; most >>> of what I know about this was picked up willy-nilly up in the 1980s and >>> '90s. For instance knowledge of color separation from writing animations >>> for the Apple II in machine code, working in a cable TV studio in the >>> 1980s, and from an art history class in college where we discussed 19th C >>> travel photos and poly/monochromatic film chemistries of the periods. >>> Later I learned fluorescence quantification from a cell biologist intent on >>> making sure we had true linear responses for readouts of f-actin mass and >>> concentration, I was fortunate to attend both a Woods Hole microscopy >>> course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 >>> training course at their offices in Cambridge, MA covered a lot of material >>> on this too. >>>> So, do people have favorite texts that cover these topics in a manner >>> digestible by new generations of students? Of biology students. Keep in >>> mind many don't know what a byte is; when I teach I ask the class if anyone >>> knows why an image is coded with white as 255 or 4095 or 16383 and >>> typically one or two hands go up but the rest of the class really doesn't >>> know. >>>> Looking forward to suggestions of easy to read definitive texts! >>>> >>>> Thank you. >>>> >>>> Cheers- >>>> >>>> >>>> ------------------------------------------------------------ >>>> This email message, including any attachments, is for the sole use of >>> the intended recipient(s) and may contain information that is proprietary, >>> confidential, and exempt from disclosure under applicable law. Any >>> unauthorized review, use, disclosure, or distribution is prohibited. If you >>> have received this email in error please notify the sender by return email >>> and delete the original message. Please note, the recipient should check >>> this email and any attachments for the presence of viruses. The >>> organization accepts no liability for any damage caused by any virus >>> transmitted by this email. >>>> ================================= >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> This message was secured via TLS by MUSC. -- Julian P.S. Smith III Director, Winthrop Microscopy Facility Dept. of Biology Winthrop University 349 Columbia Ave Rock Hill, SCÊ 29733 803-323-2111 x6427 (vox) 803-323-3448 (fax) 803-524-2347 (cell) Research Website www.birdnest.org/smithj<http://www.birdnest.org/smithj> Personal Website www.rociada-east.net<http://www.rociada-east.net> |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear Herlinde, you will find the link earlier in this thread. Best, Mike ________________________________ From: Confocal Microscopy List <[hidden email]> on behalf of Herlinde De Keersmaecker <[hidden email]> Sent: Thursday, November 22, 2018 2:26 AM To: [hidden email] Subject: Re: seeking "reliable literature" on correct imaging ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy LISTSERV 16.0 - CONFOCALMICROSCOPY List at LISTS.UMN.EDU - Listserv Lists at the University of Minnesota<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> lists.umn.edu [hidden email]: listserv archives. confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear Mike, I would also like to have this presentation to improve trainings. Thank you, Herlinde -------- Oorspronkelijk bericht -------- Onderwerp: Re: seeking "reliable literature" on correct imaging Van: "Smith, III, Julian P.S" Aan: [hidden email] Cc: ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Joining the chorus, I would love to have a copy of this powerpoint as well. Best, Julian On 11/21/18 1:56 AM, Julia Edgar wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Would love to have it too, if possible. I hope your name is pasted all over it so you get due credit. > Best wishes > Julia > > > Sent from my iPhone. Please excuse typos. > >> On 20 Nov 2018, at 22:14, Karissa Tilbury <[hidden email]> wrote: >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >> Post images on http://www.imgur.com and include the link in your posting. >> ***** >> >> Mike, >> >> I too would also appreciate this PowerPoint. I think in the context of the >> ethics thread, this is very interesting and useful conversation. My >> students are currently in the mandated ethics class and the topics >> discussed are crazy extremes that really have their roots in 'smaller' less >> obvious mistakes to most people. Focusing the discussion on what they are >> doing in the lab to protect the quality of data or understand limitations >> seems more important to me, than discussing ethics of CRISPR and human >> life. >> >> Karissa >> >> On Fri, Nov 16, 2018, 8:44 PM Ganesh Kadasoor <[hidden email] >> wrote: >> >>> ***** >>> To join, leave or search the confocal microscopy listserv, go to: >>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>> Post images on http://www.imgur.com and include the link in your posting. >>> ***** >>> >>> Hi >>> I do visit various institutions to teach basics on microscopy and imaging >>> always struggle convey the right message in the absence of a proper >>> material.. >>> Your presentation may be really a good tool for me to convey correct >>> message and make the next generation scientist fool proof.. >>> Kindly provide me the PPT .. >>> Reg >>> Ganesh Kadasoor >>> Bangalore >>> India >>> >>> >>> Sent from my iPhone >>> >>>> On 16-Nov-2018, at 11:06 PM, Lemasters, John J. <[hidden email]> >>> wrote: >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike, >>>> >>>> I would like a copy of the PowerPoint as well. This is a very important >>> issue that Michael Cammer raises. Trainees (and even more senior folks) >>> continue to make these mistakes even as you emphatically tell them not to. >>>> Thanks again, >>>> >>>> John >>>> >>>> -- >>>> John J. Lemasters, MD, PhD >>>> Professor and GlaxoSmithKline Distinguished Endowed Chair >>>> Director, Center for Cell Death, Injury & Regeneration >>>> Departments of Drug Discovery & Biomedical Sciences and Biochemistry & >>> Molecular Biology >>>> Medical University of South Carolina >>>> DD504 Drug Discovery Building >>>> 70 President Street, MSC 139 >>>> Charleston, SC 29425 >>>> >>>> Office: 843-876-2360 >>>> Lab: 843-876-2354 >>>> Fax: 843-876-2353 >>>> Email: [hidden email] >>>> http://academicdepartments.musc.edu/ccdir >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List [mailto:[hidden email]] >>> On Behalf Of Kathryn Spencer >>>> Sent: Friday, November 16, 2018 12:32 PM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> CAUTION: External >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Mike; >>>> Could I get your PowerPoint as well? I have the same issues with >>> my users. I'm "retraining" all of them with an open-software quiz, to see >>> if they understand basic concepts. Many are complaining and reluctant, >>> because they don't see the issues with their images. This after one 6-year >>> post-doc's data was totally discarded because she saved everything as >>> JPG....I certainly NEVER taught her to do THAT. >>>> Your PowerPoint should hold more credibility that I obviously >>> have.... >>>> Best; >>>> Kathy >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of MODEL, MICHAEL >>>> Sent: Friday, November 16, 2018 9:00 AM >>>> To: [hidden email] >>>> Subject: Re: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Hi Michael, >>>> >>>> We recently ran a workshop where I gave a 3-hour talk on various kinds >>> of quantification in microscopy. I can send you a PowerPoint file but don't >>> have a text. >>>> Mike Model >>>> >>>> -----Original Message----- >>>> From: Confocal Microscopy List <[hidden email]> On >>> Behalf Of Cammer, Michael >>>> Sent: Friday, November 16, 2018 11:50 AM >>>> To: [hidden email] >>>> Subject: seeking "reliable literature" on correct imaging >>>> >>>> ***** >>>> To join, leave or search the confocal microscopy listserv, go to: >>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >>>> Post images on http://www.imgur.com and include the link in your >>> posting. >>>> ***** >>>> >>>> Increasingly we have found that microscope users do not understand >>> proper imaging. >>>> A few examples: >>>> Confocal images are saturated and have the offset set to negative >>> numbers intentionally "to reduce background". >>>> Exposures are changed in fluorescent micrographs to make each one "look >>> good". >>>> 16 bit raw data with no saturation or clipping are set to 8 bits with a >>> lot of saturated and clipped pixels at the extremes and these are what are >>> considered raw data. >>>> JPG compression is great because images can be emailed. >>>> People assume (and get angry when this doesn't work) that computers can >>> automatically segment and count anything regardless of experimental design, >>> image quality, etc. >>>> Even if they have saved everything as TIF with no metadata and forgot >>> what magnifications they used. >>>> A student who recognizes these problems and wants to learn the right way >>> emailed me yesterday asking for "any reliable literature you recommend if >>> I'd like to read more about correct imaging." >>>> I did Google searches and, after skimming a bunch of web pages, realized >>> that I didn't really have an answer. I could send to this page and to this >>> page, but it's not a coherent narrative. And I don't have a library; most >>> of what I know about this was picked up willy-nilly up in the 1980s and >>> '90s. For instance knowledge of color separation from writing animations >>> for the Apple II in machine code, working in a cable TV studio in the >>> 1980s, and from an art history class in college where we discussed 19th C >>> travel photos and poly/monochromatic film chemistries of the periods. >>> Later I learned fluorescence quantification from a cell biologist intent on >>> making sure we had true linear responses for readouts of f-actin mass and >>> concentration, I was fortunate to attend both a Woods Hole microscopy >>> course and at NCSU John Russ's course on image analysis, and BioRad MRC 600 >>> training course at their offices in Cambridge, MA covered a lot of material >>> on this too. >>>> So, do people have favorite texts that cover these topics in a manner >>> digestible by new generations of students? Of biology students. Keep in >>> mind many don't know what a byte is; when I teach I ask the class if anyone >>> knows why an image is coded with white as 255 or 4095 or 16383 and >>> typically one or two hands go up but the rest of the class really doesn't >>> know. >>>> Looking forward to suggestions of easy to read definitive texts! >>>> >>>> Thank you. >>>> >>>> Cheers- >>>> >>>> >>>> ------------------------------------------------------------ >>>> This email message, including any attachments, is for the sole use of >>> the intended recipient(s) and may contain information that is proprietary, >>> confidential, and exempt from disclosure under applicable law. Any >>> unauthorized review, use, disclosure, or distribution is prohibited. If you >>> have received this email in error please notify the sender by return email >>> and delete the original message. Please note, the recipient should check >>> this email and any attachments for the presence of viruses. The >>> organization accepts no liability for any damage caused by any virus >>> transmitted by this email. >>>> ================================= >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> This message was secured via TLS by MUSC. -- Julian P.S. Smith III Director, Winthrop Microscopy Facility Dept. of Biology Winthrop University 349 Columbia Ave Rock Hill, SCÊ 29733 803-323-2111 x6427 (vox) 803-323-3448 (fax) 803-524-2347 (cell) Research Website www.birdnest.org/smithj<http://www.birdnest.org/smithj<http://www.birdnest.org/smithj<http://www.birdnest.org/smithj>> Personal Website www.rociada-east.net<http://www.rociada-east.net<http://www.rociada-east.net<http://www.rociada-east.net>> |
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