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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. ***** Sorry, I didn't mean to send this message to everyone. After I realized that I sent it to the List address, I did not click Approve, hoping it wouldn't go anywhere. But a couple days later it went through anyway -----Original Message----- From: Confocal Microscopy List <[hidden email]> On Behalf Of MODEL, MICHAEL Sent: Monday, November 19, 2018 8:52 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. ***** 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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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 Dr. Model-- Interesting. You're right: that shouldn't be happening. I'll try to see if we have a setting set incorrectly. Thanks for pointing it out-- Martin Wessendorf List Manager On 11/20/2018 4:14 PM, 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. > ***** > > Sorry, I didn't mean to send this message to everyone. After I realized that I sent it to the List address, I did not click Approve, hoping it wouldn't go anywhere. But a couple days later it went through anyway > > -----Original Message----- > From: Confocal Microscopy List <[hidden email]> On Behalf Of MODEL, MICHAEL > Sent: Monday, November 19, 2018 8:52 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. > ***** > > 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. > ================================= -- 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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