Web app to direct user to the right microscope?

[VERMEREN Matthieu]

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Dear all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

[Craig Brideau]

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I feel that you would have to ask far too many questions to account for
even the more common variables in sample type, preparation, etc. even
before you consider the equipment. I would instead consider a first-pass
"screening questionnaire" that would be forwarded to an actual microscopy
professional for followup.

Craig

On Wed, Apr 28, 2021 at 10:29 AM VERMEREN Matthieu <
[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 all,
>
> I've been repetitively asked by some users if I could build a Web app that
> would guide them through a series of questions (like a personality test) to
> the ideal microscope(s) for their experiment.  Does anyone have experience
> with this?  Which app have you used?
>
> Obviously, I'd rather they come and talk but maybe I'm just scary :-)
>
> Sincerely,
>
> Matthieu
>
> The University of Edinburgh is a charitable body, registered in Scotland,
> with registration number SC005336. Is e buidheann carthannais a th' ann an
> Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
>

[Benjamin Smith]

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*****

Along the lines of what Craig said, multimodal imaging approaches are also
best, and answers would also be dependent on the users willingness to use
non-traditional methods regardless of how easy they may be to implement
(suck as Rheinberg illumination).  Also, the user would need to be aware of
how they intend to quantify their data to know therefore how they need to
collect that data, and the resolution they need, FOV, colocalization,
multi-spectral, how many dimensions, etc.  Many times I have run into
people who collected months worth of data using the correct instrument,
only to find out the data was collected incorrectly and cannot be
quantified, resulting in needing to reacquire the entire set again
correctly.

For example, if you wanted to measure something as "simple" as
colocalization, depending on the nature of the question and resources
available you could do BiFC, fluorescence anisotropy, FRET, FCCS, super
resolution (Airy scanning, STORM, STED, GSD, etc.), CLEM, hyperspectral
microscopy, the list goes on and on.  On top of that, for each of these
modalities, there are further considerations for what probes to use
(especially for BiFC, as well as FRET and STORM) and how best to set up the
experiment.  Then comes the whole other half which is how to quantify
colocalization data, and the amount and type of information that can be
gleaned by each of these methods.

Although, I could also be grossly over complicating things, but in my
experience users often don't even know how to phrase what it is that they
want to do in terms of what the microscope is capable of, which is the
whole reason why skilled microscopists are highly sought after to help
bridge that gap.  However, if someone had the insight to condense all this
into an app a non-microscopist could easily navigate and understand, that
would be revolutionary to the field and definitely would be a major
contribution to the scientific endeavor that would be greatly appreciated
by millions!  I just hope it wouldn't encourage even more people to collect
months of worthless data, because they did not fully understand what they
were trying to do.



On Wed, Apr 28, 2021 at 9:55 AM Craig Brideau <[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.
> *****
>
> I feel that you would have to ask far too many questions to account for
> even the more common variables in sample type, preparation, etc. even
> before you consider the equipment. I would instead consider a first-pass
> "screening questionnaire" that would be forwarded to an actual microscopy
> professional for followup.
>
> Craig
>
> On Wed, Apr 28, 2021 at 10:29 AM VERMEREN Matthieu <
> [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 all,
> >
> > I've been repetitively asked by some users if I could build a Web app
> that
> > would guide them through a series of questions (like a personality test)
> to
> > the ideal microscope(s) for their experiment.  Does anyone have
> experience
> > with this?  Which app have you used?
> >
> > Obviously, I'd rather they come and talk but maybe I'm just scary :-)
> >
> > Sincerely,
> >
> > Matthieu
> >
> > The University of Edinburgh is a charitable body, registered in Scotland,
> > with registration number SC005336. Is e buidheann carthannais a th' ann
> an
> > Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
> >
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Weill Hall
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/

[Michelle Peckham]

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*****

What about making an app - based on one or more of the recent reviews: e.g. PMID: 30602772 'super-resolution microscopy demystified'?

On 28/04/2021, 17:29, "Confocal Microscopy List on behalf of VERMEREN Matthieu" <[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 all,

    I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?

    Obviously, I'd rather they come and talk but maybe I'm just scary :-)

    Sincerely,

    Matthieu

    The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

[Chew, Teng-Leong]

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*****

Dear Matthieu,

I echo the sentiments from Craig, and Ben. Creating an app seems vastly simplistic to this complicated question that at the end may not have a single ‘right answer’. In addition, this process can be rather iterative even for experienced imaging scientists.

Perhaps you can point them to a recent AIC review. I wonder if they may change their mind about an app.

‘Hypothesis-driven quantitative fluorescence microscopy – the importance of reverse-thinking in experimental design.’
https://is.gd/iC07IP

Regards,
Leong




From: Confocal Microscopy List <[hidden email]> on behalf of VERMEREN Matthieu <[hidden email]>
Reply-To: Confocal Microscopy List <[hidden email]>
Date: Wednesday, April 28, 2021 at 12:29 PM
To: "[hidden email]" <[hidden email]>
Subject: Web app to direct user to the right microscope?

External Email: Use Caution

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Post images on https://urldefense.com/v3/__http:/www.imgur.com__;!!Eh6p8Q!UO-AGYluzQp3DNoxpGCQBD5O96szp2fwSSO--MKd8HkCKS_ihc6K-IkctGNvOwqqng$  and include the link in your posting.
*****

Dear all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

[Oshel, Philip Eugene]

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*****

I'm not sure an app like this is the right approach, at least at first.
The user needs to state explicitly what is the question. The question drives the method. I often find users haven't really properly defined their question(s), so any attempt to answer "what kind of microscopy do I need" is at best premature.
Once the user has a clear statement of their question -- not what data or kind of data they're looking for, but the *question* -- they can then determine the proper controls (yes, plural; only needing one control is rare). Only after both the question(s) and controls are unambiguously determined can "what kind of microscopy?" be addressed. (And the answer may well be "None. Do 'method X' instead".)

An app that forced the user to do this would be very valuable.

-------------
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 Benjamin Smith <[hidden email]>
Reply-To: Confocal Microscopy List <[hidden email]>
Date: Wednesday, 28April, 2021 at 13:44
To: "[hidden email]" <[hidden email]>
Subject: [External] Re: Web app to direct user to the right microscope?

    *****
    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.
    *****

    Along the lines of what Craig said, multimodal imaging approaches are also
    best, and answers would also be dependent on the users willingness to use
    non-traditional methods regardless of how easy they may be to implement
    (suck as Rheinberg illumination).  Also, the user would need to be aware of
    how they intend to quantify their data to know therefore how they need to
    collect that data, and the resolution they need, FOV, colocalization,
    multi-spectral, how many dimensions, etc.  Many times I have run into
    people who collected months worth of data using the correct instrument,
    only to find out the data was collected incorrectly and cannot be
    quantified, resulting in needing to reacquire the entire set again
    correctly.

    For example, if you wanted to measure something as "simple" as
    colocalization, depending on the nature of the question and resources
    available you could do BiFC, fluorescence anisotropy, FRET, FCCS, super
    resolution (Airy scanning, STORM, STED, GSD, etc.), CLEM, hyperspectral
    microscopy, the list goes on and on.  On top of that, for each of these
    modalities, there are further considerations for what probes to use
    (especially for BiFC, as well as FRET and STORM) and how best to set up the
    experiment.  Then comes the whole other half which is how to quantify
    colocalization data, and the amount and type of information that can be
    gleaned by each of these methods.

    Although, I could also be grossly over complicating things, but in my
    experience users often don't even know how to phrase what it is that they
    want to do in terms of what the microscope is capable of, which is the
    whole reason why skilled microscopists are highly sought after to help
    bridge that gap.  However, if someone had the insight to condense all this
    into an app a non-microscopist could easily navigate and understand, that
    would be revolutionary to the field and definitely would be a major
    contribution to the scientific endeavor that would be greatly appreciated
    by millions!  I just hope it wouldn't encourage even more people to collect
    months of worthless data, because they did not fully understand what they
    were trying to do.



    On Wed, Apr 28, 2021 at 9:55 AM Craig Brideau <[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.
    > *****
    >
    > I feel that you would have to ask far too many questions to account for
    > even the more common variables in sample type, preparation, etc. even
    > before you consider the equipment. I would instead consider a first-pass
    > "screening questionnaire" that would be forwarded to an actual microscopy
    > professional for followup.
    >
    > Craig
    >
    > On Wed, Apr 28, 2021 at 10:29 AM VERMEREN Matthieu <
    > [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 all,
    > >
    > > I've been repetitively asked by some users if I could build a Web app
    > that
    > > would guide them through a series of questions (like a personality test)
    > to
    > > the ideal microscope(s) for their experiment.  Does anyone have
    > experience
    > > with this?  Which app have you used?
    > >
    > > Obviously, I'd rather they come and talk but maybe I'm just scary :-)
    > >
    > > Sincerely,
    > >
    > > Matthieu
    > >
    > > The University of Edinburgh is a charitable body, registered in Scotland,
    > > with registration number SC005336. Is e buidheann carthannais a th' ann
    > an
    > > Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
    > >
    >


    --
    Benjamin E. Smith, Ph. D.
    Imaging Specialist, Vision Science
    University of California, Berkeley
    195 Weill Hall
    Berkeley, CA  94720-3200
    Tel  [phone]
    Fax [phone]
    e-mail: [hidden email]
    https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/

[Jacqueline Ross]

*****
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*****

Dear Matthieu,

Even though I have email correspondence with equipment users prior to their training session, I am still often surprised when they show up with their samples.

For live imaging, I always meet with the person face-to-face before booking any equipment so that I can determine which system is best for them to start with and there are so many questions that need to be asked/answered.

Also, we have such a broad range of research to support in our facility, from biological/biomedical/pharmacy to materials/geology, etc. that it would be very hard to cover all options and possibilities. Plus there is always the analysis to consider and we try to take the reverse view as per the paper that Teng-Leong alluded to and advertised to this list a while ago.

I do have people asking to learn particular instrumentation as they can see all of our machines on our website. But I still ask the questions as sometimes they will ask to learn an invert (or upright) when their sample is not suitable. For example, the very confident person who requested the upright and turned up with a multiwell plate...

I think our team of experts is still the best option for helping users decide and in a timely way. We are also the ones who will be training and supporting them so we do need to know what is coming!

Kind regards,

Jacqui


From: Confocal Microscopy List <[hidden email]> On Behalf Of VERMEREN Matthieu
Sent: Thursday, April 29, 2021 4:28 AM
To: [hidden email]
Subject: Web app to direct user to the right microscope?

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting.
*****

Dear all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment. Does anyone have experience with this? Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

[Cammer, Michael-2]

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*****

Even if a sophisticated AI system could capture all the meeting and in lab experiments I have done over the last 30 years and score them, it would not have enough data for an app.  I bet if it included yor experiences too, it wouldn't be enough.

Also, one of the replies says, "[I]n my experience users often don't even know how to phrase what it is that they want to do in terms of what the microscope is capable of[.]"  They don't understand what microscopy can do.  They don't know what questions to ask.
Often they need help with the biology too.

We would have to give them a significant education just to understand the app.

And the people who do understand microscopy can read the webpages and ask a few follow-up questions to see what we offer.  Maybe they teach us stuff too.

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
[hidden email]  http://nyulmc.org/micros  http://microscopynotes.com/
Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567

________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of Jacqueline Ross <[hidden email]>
Sent: Wednesday, April 28, 2021 5:17:28 PM
To: [hidden email]
Subject: Re: Web app to direct user to the right microscope?

[EXTERNAL]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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*****

Dear Matthieu,

Even though I have email correspondence with equipment users prior to their training session, I am still often surprised when they show up with their samples.

For live imaging, I always meet with the person face-to-face before booking any equipment so that I can determine which system is best for them to start with and there are so many questions that need to be asked/answered.

Also, we have such a broad range of research to support in our facility, from biological/biomedical/pharmacy to materials/geology, etc. that it would be very hard to cover all options and possibilities. Plus there is always the analysis to consider and we try to take the reverse view as per the paper that Teng-Leong alluded to and advertised to this list a while ago.

I do have people asking to learn particular instrumentation as they can see all of our machines on our website. But I still ask the questions as sometimes they will ask to learn an invert (or upright) when their sample is not suitable. For example, the very confident person who requested the upright and turned up with a multiwell plate...

I think our team of experts is still the best option for helping users decide and in a timely way. We are also the ones who will be training and supporting them so we do need to know what is coming!

Kind regards,

Jacqui


From: Confocal Microscopy List <[hidden email]> On Behalf Of VERMEREN Matthieu
Sent: Thursday, April 29, 2021 4:28 AM
To: [hidden email]
Subject: Web app to direct user to the right microscope?

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting.
*****

Dear all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment. Does anyone have experience with this? Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

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[Benjamin Smith]

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One resource I do steer a lot of researchers to who want to learn more
about microscopy is the Molecular Expressions Microscopy Primer site.  The
descriptions and interactive tutorials are immensely helpful in helping a
lay-person understand how all the different imaging modalities work, and
what all those knobs and switches actually do.  I can say as a graduate
student who knew nothing about microscopes but whose research was heavily
reliant on getting a LSCM to work at the limits of its capacity, this site
was invaluable.  Once someone graduates past that, the "Imaging: A
Laboratory Manual" from Cold Spring Harbor is another excellent resource.

On Wed, Apr 28, 2021 at 2:48 PM Cammer, Michael <
[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.
> *****
>
> Even if a sophisticated AI system could capture all the meeting and in lab
> experiments I have done over the last 30 years and score them, it would not
> have enough data for an app.  I bet if it included yor experiences too, it
> wouldn't be enough.
>
> Also, one of the replies says, "[I]n my experience users often don't even
> know how to phrase what it is that they want to do in terms of what the
> microscope is capable of[.]"  They don't understand what microscopy can
> do.  They don't know what questions to ask.
> Often they need help with the biology too.
>
> We would have to give them a significant education just to understand the
> app.
>
> And the people who do understand microscopy can read the webpages and ask
> a few follow-up questions to see what we offer.  Maybe they teach us stuff
> too.
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
> NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY
> 10016
> [hidden email]  http://nyulmc.org/micros
> http://microscopynotes.com/
> Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567
>
> ________________________________
> From: Confocal Microscopy List <[hidden email]> on
> behalf of Jacqueline Ross <[hidden email]>
> Sent: Wednesday, April 28, 2021 5:17:28 PM
> To: [hidden email]
> Subject: Re: Web app to direct user to the right microscope?
>
> [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.
> *****
>
> Dear Matthieu,
>
> Even though I have email correspondence with equipment users prior to
> their training session, I am still often surprised when they show up with
> their samples.
>
> For live imaging, I always meet with the person face-to-face before
> booking any equipment so that I can determine which system is best for them
> to start with and there are so many questions that need to be
> asked/answered.
>
> Also, we have such a broad range of research to support in our facility,
> from biological/biomedical/pharmacy to materials/geology, etc. that it
> would be very hard to cover all options and possibilities. Plus there is
> always the analysis to consider and we try to take the reverse view as per
> the paper that Teng-Leong alluded to and advertised to this list a while
> ago.
>
> I do have people asking to learn particular instrumentation as they can
> see all of our machines on our website. But I still ask the questions as
> sometimes they will ask to learn an invert (or upright) when their sample
> is not suitable. For example, the very confident person who requested the
> upright and turned up with a multiwell plate...
>
> I think our team of experts is still the best option for helping users
> decide and in a timely way. We are also the ones who will be training and
> supporting them so we do need to know what is coming!
>
> Kind regards,
>
> Jacqui
>
>
> From: Confocal Microscopy List <[hidden email]> On
> Behalf Of VERMEREN Matthieu
> Sent: Thursday, April 29, 2021 4:28 AM
> To: [hidden email]
> Subject: Web app to direct user to the right microscope?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> Post images on http://www.imgur.com<http://www.imgur.com> and include the
> link in your posting.
> *****
>
> Dear all,
>
> I've been repetitively asked by some users if I could build a Web app that
> would guide them through a series of questions (like a personality test) to
> the ideal microscope(s) for their experiment. Does anyone have experience
> with this? Which app have you used?
>
> Obviously, I'd rather they come and talk but maybe I'm just scary :-)
>
> Sincerely,
>
> Matthieu
>
> The University of Edinburgh is a charitable body, registered in Scotland,
> with registration number SC005336. Is e buidheann carthannais a th' ann an
> Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
>
> ------------------------------------------------------------
> 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.
> =================================
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Weill Hall
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/

[VERMEREN Matthieu]

*****
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*****

Thanks all for your answers.

I take your points -and I specially agree that people should talk *before* doing the experiment and tell us what the biological problem is- but I think you have overshot the question:

I have a small set of microscopes, each with advantages and unique capabilities (colour or greyscale cameras, incubation chamber, fluorescence...).  When users come and see me, I know which microscope to direct them to.  The app would be a first guide to *my* microscopes, not to the whole of microscopy.  

Obviously, it will also tell people to come and talk...

Sincerely,

Matthieu




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of VERMEREN Matthieu
Sent: 28 April 2021 17:28
To: [hidden email]
Subject: Web app to direct user to the right microscope?

*****
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 all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

[Cammer, Michael-2]

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*****

I understand your question better, but people don't know that it is preferable to use a monochrome camera for single channel fluorescence.  Fluorescence is in color, so they ask to use a color camera.  This is obvious to them.  Measuring intensity and then pseudocoloring it?  Is that legal?  How would an app handle this?

Cheers-

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
Office: 646-501-0567 Cell: 914-309-3270  [hidden email]  
http://nyulmc.org/micros  http://microscopynotes.com/
 





-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of VERMEREN Matthieu
Sent: Thursday, April 29, 2021 5:11 AM
To: [hidden email]
Subject: Re: Web app to direct user to the right microscope?

[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.
*****

Thanks all for your answers.

I take your points -and I specially agree that people should talk *before* doing the experiment and tell us what the biological problem is- but I think you have overshot the question:

I have a small set of microscopes, each with advantages and unique capabilities (colour or greyscale cameras, incubation chamber, fluorescence...).  When users come and see me, I know which microscope to direct them to.  The app would be a first guide to *my* microscopes, not to the whole of microscopy.

Obviously, it will also tell people to come and talk...

Sincerely,

Matthieu




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of VERMEREN Matthieu
Sent: 28 April 2021 17:28
To: [hidden email]
Subject: Web app to direct user to the right microscope?

*****
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 all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

------------------------------------------------------------
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.
=================================

[cmci_concordia]

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*****

Hi Matthieu,

It looks like https://www.quiz-maker.com/ will give you something similar
to what you want? It looks like you can make your own quizzes with
questions that will tie to specific "types" (microscopes) at the end. If
you're looking to make something quick and intuitive for your specific
users, then that might be the tool. As you say, in the end people are going
to have to come and talk to you anyway, but at least this way they will
have been primed about the things they need to consider. Also, this way
*you* get to ask the questions which would lead you to pick the right
microscope for the job; "Do you need a colour camera?" is a different, and
probably less enlightening question than "Which tissue stains or
fluorophores are you using?"

Best,
Chris
________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of VERMEREN Matthieu <[hidden email]>
Sent: Thursday, April 29, 2021 5:11 AM
To: [hidden email] <[hidden email]>
Subject: Re: Web app to direct user to the right microscope?

Attention This email originates from outside the concordia.ca domain. // Ce courriel provient de l'exterieur du domaine de concordia.ca
*****
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*****

Thanks all for your answers.

I take your points -and I specially agree that people should talk *before* doing the experiment and tell us what the biological problem is- but I think you have overshot the question:

I have a small set of microscopes, each with advantages and unique capabilities (colour or greyscale cameras, incubation chamber, fluorescence...).  When users come and see me, I know which microscope to direct them to.  The app would be a first guide to *my* microscopes, not to the whole of microscopy.

Obviously, it will also tell people to come and talk...

Sincerely,

Matthieu




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of VERMEREN Matthieu
Sent: 28 April 2021 17:28
To: [hidden email]
Subject: Web app to direct user to the right microscope?

*****
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 all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

[Arvydas Matiukas]

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*****

Matthieu’s “simple” question sparked a very interesting discussion.  In my  understanding he needs a simple algorithm/app to orient and advise beginner-intermediate level non-confocal microscopy users. Such app may be useful for specific types of users and Microscopy Labs/Cores.

My Core hosts only confocals but I also supervise simple widefield microscopes as department-affiliated. In my experience the most difficult communication is with the beginner/low-experience microscopy users: I second other posts that such users often are not able correctly formulate their application and are using incorrect terms , or even worse –they insist on wrong application (because in their understanding they  were  advised in that way). Therefore in such case the app would not be efficient except giving the user some initial thought, and I would prefer live discussion and education of the user.

Intermediate level users usually correctly know their application but still may benefit from advice how to improve/optimize their sample, imaging mode and settings. I believe that the app would work best for matching such users with microscope types and applications.

Advanced users need the extreme from  state-of-the–art  microscopes or have a unique application. Therefore to achieve the best result a reiterative process of discussion and experimental imaging is needed (as was mentioned earlier). In this case the app would not work unless in includes huge knowledgebase.

Mathieu, I wanted to point you to some example algorithm that directs user to the optimal microscope, however I see only ones for the big Cores  hosting multiple  advanced and specialized microscopes.


Best regards,
Arvydas
+++++++++++++++++++++++++++++
Arvydas Matiukas, Ph.D.
Director of  Neuroscience  Microscopy Core
Manager of NRB Shared Research Equipment
SUNY Upstate Medical University


From: VERMEREN Matthieu<mailto:[hidden email]>
Sent: Thursday, April 29, 2021 5:14 AM
To: [hidden email]<mailto:[hidden email]>
Subject: [EXTERNAL] Re: Web app to direct user to the right microscope?

*****
To join, leave or search the confocal microscopy listserv, go to:
https://urldefense.com/v3/__http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy__;!!GobTDDpD7A!ffx4iFppZDIa5YpH2cKDouKzwkxPS9RyVTNP1EgxXxDQ9i5F7aBLtlS_QxILZZvviA$<https://urldefense.com/v3/__http:/lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy__;!!GobTDDpD7A!ffx4iFppZDIa5YpH2cKDouKzwkxPS9RyVTNP1EgxXxDQ9i5F7aBLtlS_QxILZZvviA$>
Post images on https://urldefense.com/v3/__http://www.imgur.com__;!!GobTDDpD7A!ffx4iFppZDIa5YpH2cKDouKzwkxPS9RyVTNP1EgxXxDQ9i5F7aBLtlS_QxKnB0lVjA$<https://urldefense.com/v3/__http:/www.imgur.com__;!!GobTDDpD7A!ffx4iFppZDIa5YpH2cKDouKzwkxPS9RyVTNP1EgxXxDQ9i5F7aBLtlS_QxKnB0lVjA$>  and include the link in your posting.
*****

Thanks all for your answers.

I take your points -and I specially agree that people should talk *before* doing the experiment and tell us what the biological problem is- but I think you have overshot the question:

I have a small set of microscopes, each with advantages and unique capabilities (colour or greyscale cameras, incubation chamber, fluorescence...).  When users come and see me, I know which microscope to direct them to.  The app would be a first guide to *my* microscopes, not to the whole of microscopy.

Obviously, it will also tell people to come and talk...

Sincerely,

Matthieu




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of VERMEREN Matthieu
Sent: 28 April 2021 17:28
To: [hidden email]
Subject: Web app to direct user to the right microscope?

*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on https://urldefense.com/v3/__http://www.imgur.com__;!!GobTDDpD7A!ffx4iFppZDIa5YpH2cKDouKzwkxPS9RyVTNP1EgxXxDQ9i5F7aBLtlS_QxKnB0lVjA$<https://urldefense.com/v3/__http:/www.imgur.com__;!!GobTDDpD7A!ffx4iFppZDIa5YpH2cKDouKzwkxPS9RyVTNP1EgxXxDQ9i5F7aBLtlS_QxKnB0lVjA$>  and include the link in your posting.
*****

Dear all,

I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?

Obviously, I'd rather they come and talk but maybe I'm just scary :-)

Sincerely,

Matthieu

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

[0000001ed7f52e4a-dmarc-request]

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

Maybe if you would go beyond the a simple App and use a sophisticated AI system, feed it with the combined knowledge of the 1000 top microscopy specialists plus 100,000 most relevant microscopy papers, it would actually come up with novel ways of doing microscopy? 
Best wishes
Andreas




Sent from the all-new AOL app for Android
 
  On Fri, 30 Apr 2021 at 12:19, Benjamin Smith<[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.
*****

One resource I do steer a lot of researchers to who want to learn more
about microscopy is the Molecular Expressions Microscopy Primer site.  The
descriptions and interactive tutorials are immensely helpful in helping a
lay-person understand how all the different imaging modalities work, and
what all those knobs and switches actually do.  I can say as a graduate
student who knew nothing about microscopes but whose research was heavily
reliant on getting a LSCM to work at the limits of its capacity, this site
was invaluable.  Once someone graduates past that, the "Imaging: A
Laboratory Manual" from Cold Spring Harbor is another excellent resource.

On Wed, Apr 28, 2021 at 2:48 PM Cammer, Michael <
[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.
> *****
>
> Even if a sophisticated AI system could capture all the meeting and in lab
> experiments I have done over the last 30 years and score them, it would not
> have enough data for an app.  I bet if it included yor experiences too, it
> wouldn't be enough.
>
> Also, one of the replies says, "[I]n my experience users often don't even
> know how to phrase what it is that they want to do in terms of what the
> microscope is capable of[.]"  They don't understand what microscopy can
> do.  They don't know what questions to ask.
> Often they need help with the biology too.
>
> We would have to give them a significant education just to understand the
> app.
>
> And the people who do understand microscopy can read the webpages and ask
> a few follow-up questions to see what we offer.  Maybe they teach us stuff
> too.
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
> NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY
> 10016
> [hidden email]  http://nyulmc.org/micros
> http://microscopynotes.com/
> Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567
>
> ________________________________
> From: Confocal Microscopy List <[hidden email]> on
> behalf of Jacqueline Ross <[hidden email]>
> Sent: Wednesday, April 28, 2021 5:17:28 PM
> To: [hidden email]
> Subject: Re: Web app to direct user to the right microscope?
>
> [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.
> *****
>
> Dear Matthieu,
>
> Even though I have email correspondence with equipment users prior to
> their training session, I am still often surprised when they show up with
> their samples.
>
> For live imaging, I always meet with the person face-to-face before
> booking any equipment so that I can determine which system is best for them
> to start with and there are so many questions that need to be
> asked/answered.
>
> Also, we have such a broad range of research to support in our facility,
> from biological/biomedical/pharmacy to materials/geology, etc. that it
> would be very hard to cover all options and possibilities. Plus there is
> always the analysis to consider and we try to take the reverse view as per
> the paper that Teng-Leong alluded to and advertised to this list a while
> ago.
>
> I do have people asking to learn particular instrumentation as they can
> see all of our machines on our website. But I still ask the questions as
> sometimes they will ask to learn an invert (or upright) when their sample
> is not suitable. For example, the very confident person who requested the
> upright and turned up with a multiwell plate...
>
> I think our team of experts is still the best option for helping users
> decide and in a timely way. We are also the ones who will be training and
> supporting them so we do need to know what is coming!
>
> Kind regards,
>
> Jacqui
>
>
> From: Confocal Microscopy List <[hidden email]> On
> Behalf Of VERMEREN Matthieu
> Sent: Thursday, April 29, 2021 4:28 AM
> To: [hidden email]
> Subject: Web app to direct user to the right microscope?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> Post images on http://www.imgur.com<http://www.imgur.com> and include the
> link in your posting.
> *****
>
> Dear all,
>
> I've been repetitively asked by some users if I could build a Web app that
> would guide them through a series of questions (like a personality test) to
> the ideal microscope(s) for their experiment. Does anyone have experience
> with this? Which app have you used?
>
> Obviously, I'd rather they come and talk but maybe I'm just scary :-)
>
> Sincerely,
>
> Matthieu
>
> The University of Edinburgh is a charitable body, registered in Scotland,
> with registration number SC005336. Is e buidheann carthannais a th' ann an
> Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
>
> ------------------------------------------------------------
> 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.
> =================================
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Weill Hall
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/
 

[Benjamin Smith]

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

I think as long as we are still surprised on by the rare occasion our most
cutting edge AI algorithms actually generate accurate results, there is a
way to go before it can be relied upon to make recommendations on
experimental design: https://www.youtube.com/watch?v=TfVYxnhuEdU

The fact that currently AI tends to generate plausible sounding results
that are wrong - that almost certainly would do more harm than good.

On Sat, May 1, 2021 at 8:01 AM Andreas Bruckbauer <
[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.
> *****
>
> Maybe if you would go beyond the a simple App and use a sophisticated AI
> system, feed it with the combined knowledge of the 1000 top microscopy
> specialists plus 100,000 most relevant microscopy papers, it would actually
> come up with novel ways of doing microscopy?
> Best wishes
> Andreas
>
>
>
>
> Sent from the all-new AOL app for Android
>
>   On Fri, 30 Apr 2021 at 12:19, Benjamin Smith<[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.
> *****
>
> One resource I do steer a lot of researchers to who want to learn more
> about microscopy is the Molecular Expressions Microscopy Primer site.  The
> descriptions and interactive tutorials are immensely helpful in helping a
> lay-person understand how all the different imaging modalities work, and
> what all those knobs and switches actually do.  I can say as a graduate
> student who knew nothing about microscopes but whose research was heavily
> reliant on getting a LSCM to work at the limits of its capacity, this site
> was invaluable.  Once someone graduates past that, the "Imaging: A
> Laboratory Manual" from Cold Spring Harbor is another excellent resource.
>
> On Wed, Apr 28, 2021 at 2:48 PM Cammer, Michael <
> [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.
> > *****
> >
> > Even if a sophisticated AI system could capture all the meeting and in
> lab
> > experiments I have done over the last 30 years and score them, it would
> not
> > have enough data for an app.  I bet if it included yor experiences too,
> it
> > wouldn't be enough.
> >
> > Also, one of the replies says, "[I]n my experience users often don't even
> > know how to phrase what it is that they want to do in terms of what the
> > microscope is capable of[.]"  They don't understand what microscopy can
> > do.  They don't know what questions to ask.
> > Often they need help with the biology too.
> >
> > We would have to give them a significant education just to understand the
> > app.
> >
> > And the people who do understand microscopy can read the webpages and ask
> > a few follow-up questions to see what we offer.  Maybe they teach us
> stuff
> > too.
> >
> > Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
> > NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY
> > 10016
> > [hidden email]  http://nyulmc.org/micros
> > http://microscopynotes.com/
> > Voice direct only, no text or messages:  1-914-309-3270 and
> 1-646-501-0567
> >
> > ________________________________
> > From: Confocal Microscopy List <[hidden email]> on
> > behalf of Jacqueline Ross <[hidden email]>
> > Sent: Wednesday, April 28, 2021 5:17:28 PM
> > To: [hidden email]
> > Subject: Re: Web app to direct user to the right microscope?
> >
> > [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.
> > *****
> >
> > Dear Matthieu,
> >
> > Even though I have email correspondence with equipment users prior to
> > their training session, I am still often surprised when they show up with
> > their samples.
> >
> > For live imaging, I always meet with the person face-to-face before
> > booking any equipment so that I can determine which system is best for
> them
> > to start with and there are so many questions that need to be
> > asked/answered.
> >
> > Also, we have such a broad range of research to support in our facility,
> > from biological/biomedical/pharmacy to materials/geology, etc. that it
> > would be very hard to cover all options and possibilities. Plus there is
> > always the analysis to consider and we try to take the reverse view as
> per
> > the paper that Teng-Leong alluded to and advertised to this list a while
> > ago.
> >
> > I do have people asking to learn particular instrumentation as they can
> > see all of our machines on our website. But I still ask the questions as
> > sometimes they will ask to learn an invert (or upright) when their sample
> > is not suitable. For example, the very confident person who requested the
> > upright and turned up with a multiwell plate...
> >
> > I think our team of experts is still the best option for helping users
> > decide and in a timely way. We are also the ones who will be training and
> > supporting them so we do need to know what is coming!
> >
> > Kind regards,
> >
> > Jacqui
> >
> >
> > From: Confocal Microscopy List <[hidden email]> On
> > Behalf Of VERMEREN Matthieu
> > Sent: Thursday, April 29, 2021 4:28 AM
> > To: [hidden email]
> > Subject: Web app to direct user to the right microscope?
> >
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> > Post images on http://www.imgur.com<http://www.imgur.com> and include
> the
> > link in your posting.
> > *****
> >
> > Dear all,
> >
> > I've been repetitively asked by some users if I could build a Web app
> that
> > would guide them through a series of questions (like a personality test)
> to
> > the ideal microscope(s) for their experiment. Does anyone have experience
> > with this? Which app have you used?
> >
> > Obviously, I'd rather they come and talk but maybe I'm just scary :-)
> >
> > Sincerely,
> >
> > Matthieu
> >
> > The University of Edinburgh is a charitable body, registered in Scotland,
> > with registration number SC005336. Is e buidheann carthannais a th' ann
> an
> > Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
> >
> > ------------------------------------------------------------
> > 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.
> > =================================
> >
>
>
> --
> Benjamin E. Smith, Ph. D.
> Imaging Specialist, Vision Science
> University of California, Berkeley
> 195 Weill Hall
> Berkeley, CA  94720-3200
> Tel  [phone]
> Fax [phone]
> e-mail: [hidden email]
>
> https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/
>
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Weill Hall
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/

[0000001ed7f52e4a-dmarc-request]

*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on http://www.imgur.com and include the link in your posting.
*****

Thanks Benjamin for the excellent video link, I can now see where this is going, scientists would let the AI generate the whole publication instead of just asking for advice on microscopy and nobody could tell the difference :-( 

Best wishes

Andreas





Sent from the all-new AOL app for Android
 
  On Sun, 2 May 2021 at 4:14, Benjamin Smith<[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.
*****

I think as long as we are still surprised on by the rare occasion our most
cutting edge AI algorithms actually generate accurate results, there is a
way to go before it can be relied upon to make recommendations on
experimental design: https://www.youtube.com/watch?v=TfVYxnhuEdU

The fact that currently AI tends to generate plausible sounding results
that are wrong - that almost certainly would do more harm than good.

On Sat, May 1, 2021 at 8:01 AM Andreas Bruckbauer <
[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.
> *****
>
> Maybe if you would go beyond the a simple App and use a sophisticated AI
> system, feed it with the combined knowledge of the 1000 top microscopy
> specialists plus 100,000 most relevant microscopy papers, it would actually
> come up with novel ways of doing microscopy?
> Best wishes
> Andreas
>
>
>
>
> Sent from the all-new AOL app for Android
>
>  On Fri, 30 Apr 2021 at 12:19, Benjamin Smith<[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.
> *****
>
> One resource I do steer a lot of researchers to who want to learn more
> about microscopy is the Molecular Expressions Microscopy Primer site.  The
> descriptions and interactive tutorials are immensely helpful in helping a
> lay-person understand how all the different imaging modalities work, and
> what all those knobs and switches actually do.  I can say as a graduate
> student who knew nothing about microscopes but whose research was heavily
> reliant on getting a LSCM to work at the limits of its capacity, this site
> was invaluable.  Once someone graduates past that, the "Imaging: A
> Laboratory Manual" from Cold Spring Harbor is another excellent resource.
>
> On Wed, Apr 28, 2021 at 2:48 PM Cammer, Michael <
> [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.
> > *****
> >
> > Even if a sophisticated AI system could capture all the meeting and in
> lab
> > experiments I have done over the last 30 years and score them, it would
> not
> > have enough data for an app.  I bet if it included yor experiences too,
> it
> > wouldn't be enough.
> >
> > Also, one of the replies says, "[I]n my experience users often don't even
> > know how to phrase what it is that they want to do in terms of what the
> > microscope is capable of[.]"  They don't understand what microscopy can
> > do.  They don't know what questions to ask.
> > Often they need help with the biology too.
> >
> > We would have to give them a significant education just to understand the
> > app.
> >
> > And the people who do understand microscopy can read the webpages and ask
> > a few follow-up questions to see what we offer.  Maybe they teach us
> stuff
> > too.
> >
> > Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
> > NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY
> > 10016
> > [hidden email]  http://nyulmc.org/micros
> > http://microscopynotes.com/
> > Voice direct only, no text or messages:  1-914-309-3270 and
> 1-646-501-0567
> >
> > ________________________________
> > From: Confocal Microscopy List <[hidden email]> on
> > behalf of Jacqueline Ross <[hidden email]>
> > Sent: Wednesday, April 28, 2021 5:17:28 PM
> > To: [hidden email]
> > Subject: Re: Web app to direct user to the right microscope?
> >
> > [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.
> > *****
> >
> > Dear Matthieu,
> >
> > Even though I have email correspondence with equipment users prior to
> > their training session, I am still often surprised when they show up with
> > their samples.
> >
> > For live imaging, I always meet with the person face-to-face before
> > booking any equipment so that I can determine which system is best for
> them
> > to start with and there are so many questions that need to be
> > asked/answered.
> >
> > Also, we have such a broad range of research to support in our facility,
> > from biological/biomedical/pharmacy to materials/geology, etc. that it
> > would be very hard to cover all options and possibilities. Plus there is
> > always the analysis to consider and we try to take the reverse view as
> per
> > the paper that Teng-Leong alluded to and advertised to this list a while
> > ago.
> >
> > I do have people asking to learn particular instrumentation as they can
> > see all of our machines on our website. But I still ask the questions as
> > sometimes they will ask to learn an invert (or upright) when their sample
> > is not suitable. For example, the very confident person who requested the
> > upright and turned up with a multiwell plate...
> >
> > I think our team of experts is still the best option for helping users
> > decide and in a timely way. We are also the ones who will be training and
> > supporting them so we do need to know what is coming!
> >
> > Kind regards,
> >
> > Jacqui
> >
> >
> > From: Confocal Microscopy List <[hidden email]> On
> > Behalf Of VERMEREN Matthieu
> > Sent: Thursday, April 29, 2021 4:28 AM
> > To: [hidden email]
> > Subject: Web app to direct user to the right microscope?
> >
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> > Post images on http://www.imgur.com<http://www.imgur.com> and include
> the
> > link in your posting.
> > *****
> >
> > Dear all,
> >
> > I've been repetitively asked by some users if I could build a Web app
> that
> > would guide them through a series of questions (like a personality test)
> to
> > the ideal microscope(s) for their experiment. Does anyone have experience
> > with this? Which app have you used?
> >
> > Obviously, I'd rather they come and talk but maybe I'm just scary :-)
> >
> > Sincerely,
> >
> > Matthieu
> >
> > The University of Edinburgh is a charitable body, registered in Scotland,
> > with registration number SC005336. Is e buidheann carthannais a th' ann
> an
> > Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
> >
> > ------------------------------------------------------------
> > 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.
> > =================================
> >
>
>
> --
> Benjamin E. Smith, Ph. D.
> Imaging Specialist, Vision Science
> University of California, Berkeley
> 195 Weill Hall
> Berkeley, CA  94720-3200
> Tel  [phone]
> Fax [phone]
> e-mail: [hidden email]
>
> https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/
>
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Weill Hall
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/
 

[Strambio, Caterina]

*****
To join, leave or search the confocal microscopy listserv, go to:
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*****

Dear All

I am not totally sure I understand the initial question. Please let me know if I am totally off topic.

If the question is how to help the user learn about Microscopy instrumentation and virtually design/build a Microscope that would fit a given experimental design, our recently developed Micro-Meta App might be an initial answer.

The primary purpose of Micro-Meta App (we are writing up the paper as we speak) is for microscope custodians and users to easily collect microscopy metadata (hardware specification, settings, configurations) to facilitate proper experimental documentation.

However, Micro-Meta App can also be used for training purposes to help users and students learn about the microscope they are using etc.

In this sense,  Micro-Meta App might help in the task at the basis of this thread.

I am happy to learn more about the specific use case being discussed
If you are interested please take a look.

Cheers

Caterina

---

Website:
https://wu-bimac.github.io/MicroMetaApp.github.io/

GitHub release
https://github.com/WU-BIMAC/MicroMetaApp-Electron/releases/tag/1.0.0-b1-2

Read the Docs documentation
https://micrometaapp-docs.readthedocs.io/en/latest/

> On Apr 28, 2021, at 14:03, Chew, Teng-Leong <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy&amp;data=04%7C01%7Ccaterina.strambio%40UMASSMED.EDU%7Cb3a53aee12364bc873ae08d90a713ebd%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C637552303762538289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=wlzZz8ltgM06gAoFR2f2EQJKK6fIGG8W3%2FD%2BAvqeorY%3D&amp;reserved=0
> Post images on https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imgur.com%2F&amp;data=04%7C01%7Ccaterina.strambio%40UMASSMED.EDU%7Cb3a53aee12364bc873ae08d90a713ebd%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C637552303762538289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=sVWaUl9wPMUgpl56DYki%2FFl0nJHhgwoTqimsR8%2FG%2Bag%3D&amp;reserved=0 and include the link in your posting.
> *****
>
> Dear Matthieu,
>
> I echo the sentiments from Craig, and Ben. Creating an app seems vastly simplistic to this complicated question that at the end may not have a single ‘right answer’. In addition, this process can be rather iterative even for experienced imaging scientists.
>
> Perhaps you can point them to a recent AIC review. I wonder if they may change their mind about an app.
>
> ‘Hypothesis-driven quantitative fluorescence microscopy – the importance of reverse-thinking in experimental design.’
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fis.gd%2FiC07IP&amp;data=04%7C01%7Ccaterina.strambio%40UMASSMED.EDU%7Cb3a53aee12364bc873ae08d90a713ebd%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C637552303762538289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=mpntuboXrDF0s1%2FBPpvku1FZ6ixzEcIsG%2Fi5M0yYK5Q%3D&amp;reserved=0
>
> Regards,
> Leong
>
>
>
>
> From: Confocal Microscopy List <[hidden email]> on behalf of VERMEREN Matthieu <[hidden email]>
> Reply-To: Confocal Microscopy List <[hidden email]>
> Date: Wednesday, April 28, 2021 at 12:29 PM
> To: "[hidden email]" <[hidden email]>
> Subject: Web app to direct user to the right microscope?
>
> External Email: Use Caution
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Flists.umn.edu%2Fcgi-bin%2Fwa%3FA0%3Dconfocalmicroscopy__%3B!!Eh6p8Q!UO-AGYluzQp3DNoxpGCQBD5O96szp2fwSSO--MKd8HkCKS_ihc6K-IkctGOOhjCzsQ%24&amp;data=04%7C01%7Ccaterina.strambio%40UMASSMED.EDU%7Cb3a53aee12364bc873ae08d90a713ebd%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C637552303762538289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=lgvnYKVicfkEOZuHuDCwkMYvpgdxILZ1qRxLeRQNh%2FA%3D&amp;reserved=0 
> Post images on https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fwww.imgur.com__%3B!!Eh6p8Q!UO-AGYluzQp3DNoxpGCQBD5O96szp2fwSSO--MKd8HkCKS_ihc6K-IkctGNvOwqqng%24&amp;data=04%7C01%7Ccaterina.strambio%40UMASSMED.EDU%7Cb3a53aee12364bc873ae08d90a713ebd%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C637552303762538289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=6JVUIFR2QTV8ljas4PccIzdIsEKxWgQ8x%2F%2BL7b9F3%2Bw%3D&amp;reserved=0  and include the link in your posting.
> *****
>
> Dear all,
>
> I've been repetitively asked by some users if I could build a Web app that would guide them through a series of questions (like a personality test) to the ideal microscope(s) for their experiment.  Does anyone have experience with this?  Which app have you used?
>
> Obviously, I'd rather they come and talk but maybe I'm just scary :-)
>
> Sincerely,
>
> Matthieu
>
> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
>
>