New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

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Alison J. North Alison J. North
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New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

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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
Mike Nelson Mike Nelson
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Re: New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

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Post images on http://www.imgur.com and include the link in your posting.
*****

This looks really nice, thanks!

*Down with dynamite plots.

Cheers,
Mike

On Tue, Mar 31, 2020 at 1:41 PM Alison J. North <[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.
> *****
>
> 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
>
Jacqui Ross Jacqui Ross
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Re: New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

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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 Alison for this.

All online learning resources are very much appreciated at this time.

Stay safe everyone. Kia kaha/noho ora mai

Kind regards,

Jacqui

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Alison J. North
Sent: Wednesday, April 1, 2020 9:41 AM
To: [hidden email]
Subject: 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
Jonkman, James Jonkman, James
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Re: New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

In reply to this post by Alison J. North
*****
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, 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: 416-581-8593
   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


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Ana Maluenda Ana Maluenda
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Re: New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

*****
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Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Alison and James,

Thanks for sharing! This is really useful and informative.

Hope you are all staying safe and well.

Kind regards,

Ana


Ana Maluenda
Research Assistant/Laboratory Manager
Atherothrombosis and Vascular Biology Laboratory

Baker Heart and Diabetes Institute
75 Commercial Road, Melbourne VIC 3004
P (03) 8532 1359 E [hidden email] W www.baker.edu.au

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Jonkman, James
Sent: Wednesday, 1 April 2020 8:40 AM
To: [hidden email]
Subject: Re: 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.
*****

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: 416-581-8593
   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


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Michelle Peckham Michelle Peckham
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Re: New practical tutorial on quantitative confocal microscopy now out in Nature Methods!

In reply to this post by Alison J. North
*****
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*****

Great paper!

Should be required reading.

I like the concluding remarks too...

All best

Michelle

On 31/03/2020, 21:41, "Confocal Microscopy List on behalf of Alison J. North" <[hidden email] on behalf of [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.
    *****
   
    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