Re: New practical tutorial on quantitative confocal microscopy now out in Nature Protocols!

[Jonkman, James]

*****
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 to Joachim Greiner (University Heart Center Freiburg) for his keen eye and the very gracious way he pointed out to me that the accompanying poster has a couple of typos!  He said:

" I really enjoyed reading your tutorial, it was a great refresher on many important points - thanks for putting out this tutorial!!  There's one little thing I noticed, which at this time may still be useful/fixable and not just an annoying comment: A tiny typo may have slipped onto the poster, for the confocal penetration depth and serial sectioning in 2) and 3), it probably should say 'µm' instead of 'mm'.  Sorry if you've already heard it 1000x times - nevertheless, we'll print the poster and put it near our microscopes :)"

These crept in at some point with a font change.  The NatProt editors have informed me that they will be able to correct the online version likely by middle of next week, so if you haven't yet printed it please hold off until that has been corrected and download a fresh version!

Cheers,
James

-----------------------------------------------
   James Jonkman, Staff Scientist
   Advanced Optical Microscopy Facility (AOMF)
   and Wright Cell Imaging Facility (WCIF)
   University Health Network
   MaRS, PMCRT tower, 101 College St., Room 15-305
   Toronto, ON, CANADA    M5G 1L7
  [hidden email]  Tel: [phone]
   www.aomf.ca




-----Original Message-----
From: Jonkman, James
Sent: Tuesday, March 31, 2020 5:40 PM
To: Confocal Microscopy List <[hidden email]>
Subject: RE: New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

Hi, all.  It looks like the links got messed up in Alison's email.  Let me try again!

You can download a PDF via the following link, if you have institutional access to Nature Protocols:
https://www.nature.com/articles/s41596-020-0313-9

If you don't have full access, you can still view a full copy via this SharedIt link:
https://rdcu.be/b3ko0

Or feel free to email me and I'll send you a PDF.  Personally, I still can't get used to the title.  For the nearly 2 years that we worked on this paper, the working title was, "The Quagmire of Quantitative Confocal Microscopy".   There are so many pitfalls, is it even possible (especially for a new student) to get quantitative data!?  I presented a talk with this title at the Frontiers in Microscopy meeting that Leong Chew hosted at Janelia (Feb, 2018), particularly addressing the instrumentation issues at that time. As Alison said it ballooned into a much longer treatise on all the ways that things can go wrong from sample prep to analysis and stats.  However, at the last minute the NatProt editors convinced us to change the title to something that gave a more positive tone, avoided the little-known word, "quagmire", and didn't invoke images of a vulgar character from the Family Guy as any google hit of the word "quagmire" will pull up.  So "Tutorial: Guidance for quantitative confocal microscopy" it is!  I look forward to your feedback.  Stay safe everybody!

Cheers,
James


-----------------------------------------------
   James Jonkman, Staff Scientist
   Advanced Optical Microscopy Facility (AOMF)
   and Wright Cell Imaging Facility (WCIF)
   University Health Network
   MaRS, PMCRT tower, 101 College St., Room 15-305
   Toronto, ON, CANADA    M5G 1L7
  [hidden email]  Tel: [phone]
   www.aomf.ca



-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Alison J. North
Sent: Tuesday, March 31, 2020 4:41 PM
To: [hidden email]
Subject: [External] New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

*****
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 fellow microscopists,

We are delighted to announce the publication of a new "Tutorial: guidance for quantitative confocal microscopy" in Nature Protocols, compiled by James Jonkman, Claire Brown, Graham Wright, Kurt Anderson and Alison North.  This paper, which somehow gradually transformed from a small practical guide into quite an epic, was spearheaded by James Jonkman and ended up as a collaboration by facility heads across three continents.   We hope that you will find it a useful addition to the reading material you hand out to your confocal microscopy trainees - obviously it cannot compare to our still-beloved Pawley confocal handbook but it is a lot quicker to read!  There will undoubtedly be parts that some of you won't agree with - truth be told, we often disagreed amongst ourselves, ha ha, but we trust that these animated discussions led to a fairer and more representative consensus in the end!  We hope that this will provide some light reading for your facility users and other imaging scientists while they are tied to home, as well as a good introduction for future new microscopists.  It's worth noting that much of the paper is not only useful for confocal microscopy - the sections on specimen preparation, choosing the right microscope, statistics, and pilot projects, among others, should also appeal to those foraying into other microscopy techniques.  In addition, we listed almost 100 references pointing people to more in depth reading on many of the topics.

You can download a PDF via the following link, if you have institutional access to Nature Protocols:

https://www.nature.com/articles/s41596-020-0313-9

If you don't have full access, you can still view a full copy via this SharedIt link (https://rdcu.be/b3ko0<https://urldefense.proofpoint.com/v2/url?u=https-3A__rdcu.be_b3ko0&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=RBx0-WJrAO5vwSOLNmFbqYvikvIZS5ns3-USwvMOuLo&m=r6iuWA3giW4k5tQGtW0zUn4RoMDOmsT3tilY2MRvuy4&s=uaLFjZqwbnNztkoEWPrUmw4unw8TBfsLT-KYBavPL0w&e=>) and/or contact the authors for a copy.

Happy reading and imaging, and stay safe at home, wherever you are!

James, Claire, Graham, Kurt and Alison


This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.

[Oshel, Philip Eugene]

*****
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.
*****

Waiting may not be necessary. I downloaded the poster and edited it with Adobe Acrobat, the full version, not Acrobat Reader.

Very nice, thank you to the authors for making this available! I'll be putting it up in our confocal rooms.

Phil
-------------
Philip Oshel    
Imaging Facility Director
Biology Department
1304 Biosciences
1455 Calumet Ct.
Central Michigan University
Mt. Pleasant, MI 48859
989 774-3576 office

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> on behalf of "Jonkman, James" <[hidden email]>
Reply-To: Confocal Microscopy List <[hidden email]>
Date: Thursday,  02April, 2020 at 11:01
To: "[hidden email]" <[hidden email]>
Subject: Re: New practical tutorial on quantitative confocal microscopy now out in Nature Protocols!

    *****
    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 to Joachim Greiner (University Heart Center Freiburg) for his keen eye and the very gracious way he pointed out to me that the accompanying poster has a couple of typos!  He said:
   
    " I really enjoyed reading your tutorial, it was a great refresher on many important points - thanks for putting out this tutorial!!  There's one little thing I noticed, which at this time may still be useful/fixable and not just an annoying comment: A tiny typo may have slipped onto the poster, for the confocal penetration depth and serial sectioning in 2) and 3), it probably should say 'µm' instead of 'mm'.  Sorry if you've already heard it 1000x times - nevertheless, we'll print the poster and put it near our microscopes :)"
   
    These crept in at some point with a font change.  The NatProt editors have informed me that they will be able to correct the online version likely by middle of next week, so if you haven't yet printed it please hold off until that has been corrected and download a fresh version!
   
    Cheers,
    James
   
    -----------------------------------------------
       James Jonkman, Staff Scientist
       Advanced Optical Microscopy Facility (AOMF)
       and Wright Cell Imaging Facility (WCIF)
       University Health Network
       MaRS, PMCRT tower, 101 College St., Room 15-305
       Toronto, ON, CANADA    M5G 1L7
      [hidden email]  Tel: [phone]
       www.aomf.ca
   
   
   
   
    -----Original Message-----
    From: Jonkman, James
    Sent: Tuesday, March 31, 2020 5:40 PM
    To: Confocal Microscopy List <[hidden email]>
    Subject: RE: New practical tutorial on quantitative confocal microscopy now out in Nature Methods!
   
    Hi, all.  It looks like the links got messed up in Alison's email.  Let me try again!
   
    You can download a PDF via the following link, if you have institutional access to Nature Protocols:
    https://www.nature.com/articles/s41596-020-0313-9
   
    If you don't have full access, you can still view a full copy via this SharedIt link:
    https://rdcu.be/b3ko0
   
    Or feel free to email me and I'll send you a PDF.  Personally, I still can't get used to the title.  For the nearly 2 years that we worked on this paper, the working title was, "The Quagmire of Quantitative Confocal Microscopy".   There are so many pitfalls, is it even possible (especially for a new student) to get quantitative data!?  I presented a talk with this title at the Frontiers in Microscopy meeting that Leong Chew hosted at Janelia (Feb, 2018), particularly addressing the instrumentation issues at that time. As Alison said it ballooned into a much longer treatise on all the ways that things can go wrong from sample prep to analysis and stats.  However, at the last minute the NatProt editors convinced us to change the title to something that gave a more positive tone, avoided the little-known word, "quagmire", and didn't invoke images of a vulgar character from the Family Guy as any google hit of the word "quagmire" will pull up.  So "Tutorial: Guidance for quantitative confocal microscopy" it is!  I look forward to your feedback.  Stay safe everybody!
   
    Cheers,
    James
   
   
    -----------------------------------------------
       James Jonkman, Staff Scientist
       Advanced Optical Microscopy Facility (AOMF)
       and Wright Cell Imaging Facility (WCIF)
       University Health Network
       MaRS, PMCRT tower, 101 College St., Room 15-305
       Toronto, ON, CANADA    M5G 1L7
      [hidden email]  Tel: [phone]
       www.aomf.ca
   
   
   
    -----Original Message-----
    From: Confocal Microscopy List <[hidden email]> On Behalf Of Alison J. North
    Sent: Tuesday, March 31, 2020 4:41 PM
    To: [hidden email]
    Subject: [External] New practical tutorial on quantitative confocal microscopy now out in Nature Methods!
   
    *****
    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 fellow microscopists,
   
    We are delighted to announce the publication of a new "Tutorial: guidance for quantitative confocal microscopy" in Nature Protocols, compiled by James Jonkman, Claire Brown, Graham Wright, Kurt Anderson and Alison North.  This paper, which somehow gradually transformed from a small practical guide into quite an epic, was spearheaded by James Jonkman and ended up as a collaboration by facility heads across three continents.   We hope that you will find it a useful addition to the reading material you hand out to your confocal microscopy trainees - obviously it cannot compare to our still-beloved Pawley confocal handbook but it is a lot quicker to read!  There will undoubtedly be parts that some of you won't agree with - truth be told, we often disagreed amongst ourselves, ha ha, but we trust that these animated discussions led to a fairer and more representative consensus in the end!  We hope that this will provide some light reading for your facility users and other imaging scientists while they are tied to home, as well as a good introduction for future new microscopists.  It's worth noting that much of the paper is not only useful for confocal microscopy - the sections on specimen preparation, choosing the right microscope, statistics, and pilot projects, among others, should also appeal to those foraying into other microscopy techniques.  In addition, we listed almost 100 references pointing people to more in depth reading on many of the topics.
   
    You can download a PDF via the following link, if you have institutional access to Nature Protocols:
   
    https://www.nature.com/articles/s41596-020-0313-9
   
    If you don't have full access, you can still view a full copy via this SharedIt link (https://rdcu.be/b3ko0<https://urldefense.proofpoint.com/v2/url?u=https-3A__rdcu.be_b3ko0&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=RBx0-WJrAO5vwSOLNmFbqYvikvIZS5ns3-USwvMOuLo&m=r6iuWA3giW4k5tQGtW0zUn4RoMDOmsT3tilY2MRvuy4&s=uaLFjZqwbnNztkoEWPrUmw4unw8TBfsLT-KYBavPL0w&e=>) and/or contact the authors for a copy.
   
    Happy reading and imaging, and stay safe at home, wherever you are!
   
    James, Claire, Graham, Kurt and Alison
   
   
    This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
    Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
    If you have received this e-mail in error, please contact the sender and delete all copies.
    Opinions, conclusions or other information contained in this e-mail may not be that of the organization.
   
    If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
    (1) Follow any unsubscribe process the sender has included in their email
    (2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
    Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.