User Interfaces in Microscopy, Coding for Microscopy

[Kathleen Pullin]

***** 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 started attending JavaScript meetups for help picking a framework for a game I'm writing (I just finished a code school bootcamp, and I'm writing a game, gee, ....)

At the meetups there were concepts that I explained from my background in microscopy (robotics and screen interactions, frequency distributions, 3D manipulators, lots of math), and the coders were interested in what is going on in the field. When asked to do a talk on programming in microscopy, I said, "Sure, put me down." Now I realize it's like I offered to talk about the history of Earth, and I'm trying to narrow it down to a one hour presentation on 4.5 billion years of geology, or maybe 3.5 billion of biology, or maybe the evolution of humans....

Does anyone have a suggestion for a specific topic on programming and microscopy of high relevancy to front end coders?

Thanks!

Kleo Pullin

[George McNamara]

***** 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 Kleo,

Micro-Manager API enables interaction with a lot of microscope equipment with Fiji ImageJ https://fiji.sc and MatLab. I see Arduino in the list (2 items), though no Raspberry Pi (an opportunity for someone in your audience?)

https://micro-manager.org/wiki/Device_Support

A recent article in Scienceon Arduino and Raspberry Pi is

http://science.sciencemag.org/content/353/6306/1360.full

Summary

Many science research projects rely on specialized electronic devices and software to gather data that often come with a high price tag. Advances in open-source hardware and software are occurring at an astounding rate, but scientists are often slow to take advantage of these for purposes beyond their original scope. Here, we advocate that open-source technology can be easily applied in science research to collect large data sets, at the same time reducing costs and increasing the repeatability of experiments.

See also

Lego Ideas microscope  https://ideas.lego.com/projects/44370

Foldscope http://www.foldscope.com/

Low cost microscope (see other papers by RRK for low cost endoscopes, etc

http://kortum.rice.edu/uploadedFiles/Kortum/Publications/2010/Portable.pdf

With respect to RRK - class of 2016 Macarthur fellow https://www.macfound.org/fellows/970/ -

congratulations to RRK, her lab, former lab. See also http://www.rice360.rice.edu -- a lot of opportunities to innovate microscopy for global health impact (malaria and cancer diagnoses, etc).

enjoy,

George

On 9/29/2016 11:34 AM, Kathleen Pullin 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 started attending JavaScript meetups for help picking a framework for a game I'm writing (I just finished a code school bootcamp, and I'm writing a game, gee, ....)

At the meetups there were concepts that I explained from my background in microscopy (robotics and screen interactions, frequency distributions, 3D manipulators, lots of math), and the coders were interested in what is going on in the field. When asked to do a talk on programming in microscopy, I said, "Sure, put me down." Now I realize it's like I offered to talk about the history of Earth, and I'm trying to narrow it down to a one hour presentation on 4.5 billion years of geology, or maybe 3.5 billion of biology, or maybe the evolution of humans....

Does anyone have a suggestion for a specific topic on programming and microscopy of high relevancy to front end coders?

Thanks!

Kleo Pullin

[Marc Reinig]

*****
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.
*****

Thinking about how the interface will be used in situ.

Generally, user interfaces are designed to be used by a human user.
But  often we need to interface several programs for automation
purposes.  So thought should be put in to how other programs might
control the system programmatically without human intervention i.e.,
messaging, shared memory, files.

Also, its nice if you can have a configuration file to allow the user
to select one of a set configurations each having the correct
predetermined values  for common situations instead of having to enter
them one by one every time.

Marco

Marc R. Reinig
W. M. Keck Center for Adaptive Optical Microscopy
University of California Santa Cruz



On Thu, Sep 29, 2016 at 9:34 AM, Kathleen Pullin
<[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 started attending JavaScript meetups for help picking a framework for a
> game I'm writing (I just finished a code school bootcamp, and I'm writing a
> game, gee, ....)
>
> At the meetups there were concepts that I explained from my background in
> microscopy (robotics and screen interactions, frequency distributions, 3D
> manipulators, lots of math), and the coders were interested in what is going
> on in the field. When asked to do a talk on programming in microscopy, I
> said, "Sure, put me down." Now I realize it's like I offered to talk about
> the history of Earth, and I'm trying to narrow it down to a one hour
> presentation on 4.5 billion years of geology, or maybe 3.5 billion of
> biology, or maybe the evolution of humans....
>
> Does anyone have a suggestion for a specific topic on programming and
> microscopy of high relevancy to front end coders?
>
> Thanks!
>
> Kleo Pullin
>
>
> Las Vegas, Nevada
> 209-610-0555
> [hidden email]
> https://www.linkedin.com/in/kleopullin
> https://twitter.com/resolvingdust

[Barbara Foster]

***** 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. ***** Yup... I've seen this problem before! 

I think one of the most important advances in programming is the ability to interface so many different technologies (cameras, lasers or filter wheels, shutters, image acquisition/storage/processing, etc, etc etc).  There are two issues: (a) getting these technologies to communicate seamlessly and (b) making it easy for the end-user. 

A good example is the rise of optogenetics.  No longer is there just a PI in biology and perhaps a group of grad students working on a project, now each research project requires that.. plus physicists, chemists, LIMS and IT specialists... the list goes on. The microscopes are enormous multiphotons on a gantry, with treadmills for stages, video screens to introduce stimuli, and lasers, electrical leads, etc. to conduct the experiment.  Developing software to integrate, store, process, display and assist in the interpretation all of that information is huge.  And speaking of which, so are the data sets. 

You could show just 1 image of an optogenetics experiment and perhaps 1 figure from any of Deisseroth's papers... and keep the audience busy for an hour.  ...  Reminds me of clever presentation by Dr. Olga Flint, a master Food microscopist.  She showed 1 slide: a cross section of sausage.  With it, she discussed the analysis of fats, fillers, casings, etc.  At the end of 45 minutes she pointed to one small blue structure in the corner.  "And that," she proclaimed, "is the meat." 

Good hunting!
Barbara Foster, President & Chief Consultant
Microscopy/Microscopy Education  ... "Education, not Training"
www.MicroscopyEducation.com
P: 972-924-5310

Microscopy/Microscopy Education is a division of The Microscopy & Imaging Place, Inc.


NEW!   Getting involved in Raman or FTIR?
MME is now offering courses in these areas specifically for microscopists! 
Now scheduling courses through the mid 2017.  We can customize a course on nearly any topic, from fluorescence to confocal to image analysis to SEM/TEM. 
Call today for a free training evaluation.
 
At 01:41 PM 9/29/2016, Kathleen Pullin 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 started attending JavaScript meetups for help picking a framework for a game I'm writing (I just finished a code school bootcamp, and I'm writing a game, gee, ....)

At the meetups there were concepts that I explained from my background in microscopy (robotics and screen interactions, frequency distributions, 3D manipulators, lots of math), and the coders were interested in what is going on in the field. When asked to do a talk on programming in microscopy, I said, "Sure, put me down." Now I realize it's like I offered to talk about the history of Earth, and I'm trying to narrow it down to a one hour presentation on 4.5 billion years of geology, or maybe 3.5 billion of biology, or maybe the evolution of humans....

Does anyone have a suggestion for a specific topic on programming and microscopy of high relevancy to front end coders?

Thanks!

Kleo Pullin


Las Vegas, Nevada
209-610-0555
[hidden email]
https://www.linkedin.com/in/kleopullin
https://twitter.com/resolvingdust

[phil laissue-2]

***** 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 find this a highly relevant publication:

A call for bioimaging software usability

Anne E Carpenter, Lee Kamentsky & Kevin W Eliceiri

Nat Methods. 2012 Jun 28;9(7):666-70. doi: 10.1038/nmeth.2073.

Bioimaging software developed in a research setting often is not widely used by the scientific community. We suggest that, to maximize both the public’s and researchers’ investments, usability should be a more highly valued goal. We describe specific characteristics of usability toward which bioimaging software projects should aim.

PMID:

 

22743771

 

On 30 September 2016 at 00:54, Barbara Foster <[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. *****

Yup... I've seen this problem before! 

I think one of the most important advances in programming is the ability to interface so many different technologies (cameras, lasers or filter wheels, shutters, image acquisition/storage/processing, etc, etc etc).  There are two issues: (a) getting these technologies to communicate seamlessly and (b) making it easy for the end-user. 

A good example is the rise of optogenetics.  No longer is there just a PI in biology and perhaps a group of grad students working on a project, now each research project requires that.. plus physicists, chemists, LIMS and IT specialists... the list goes on. The microscopes are enormous multiphotons on a gantry, with treadmills for stages, video screens to introduce stimuli, and lasers, electrical leads, etc. to conduct the experiment.  Developing software to integrate, store, process, display and assist in the interpretation all of that information is huge.  And speaking of which, so are the data sets. 

You could show just 1 image of an optogenetics experiment and perhaps 1 figure from any of Deisseroth's papers... and keep the audience busy for an hour.  ...  Reminds me of clever presentation by Dr. Olga Flint, a master Food microscopist.  She showed 1 slide: a cross section of sausage.  With it, she discussed the analysis of fats, fillers, casings, etc.  At the end of 45 minutes she pointed to one small blue structure in the corner.  "And that," she proclaimed, "is the meat." 

Good hunting!
Barbara Foster, President & Chief Consultant
Microscopy/Microscopy Education  ... "Education, not Training"
www.MicroscopyEducation.com
P: <a href="tel:[phone]" value="[phone]" target="_blank">972-924-5310

Microscopy/Microscopy Education is a division of The Microscopy & Imaging Place, Inc.


NEW!   Getting involved in Raman or FTIR?
MME is now offering courses in these areas specifically for microscopists! 
Now scheduling courses through the mid 2017.  We can customize a course on nearly any topic, from fluorescence to confocal to image analysis to SEM/TEM. 
Call today for a free training evaluation.
 
At 01:41 PM 9/29/2016, Kathleen Pullin 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 started attending JavaScript meetups for help picking a framework for a game I'm writing (I just finished a code school bootcamp, and I'm writing a game, gee, ....)

At the meetups there were concepts that I explained from my background in microscopy (robotics and screen interactions, frequency distributions, 3D manipulators, lots of math), and the coders were interested in what is going on in the field. When asked to do a talk on programming in microscopy, I said, "Sure, put me down." Now I realize it's like I offered to talk about the history of Earth, and I'm trying to narrow it down to a one hour presentation on 4.5 billion years of geology, or maybe 3.5 billion of biology, or maybe the evolution of humans....

Does anyone have a suggestion for a specific topic on programming and microscopy of high relevancy to front end coders?

Thanks!

Kleo Pullin


Las Vegas, Nevada
<a href="tel:[phone]" value="[phone]" target="_blank">209-610-0555
[hidden email]
https://www.linkedin.com/in/kleopullin
https://twitter.com/resolvingdust

[Kevin Ryan-3]

***** 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. *****

You could discuss the transitions between experimental systems - tool box collections, deep knowledge required, and later more consumer oriented programs - simpler and more visual interfaces, fewer options that incorporate developed best practices.

Challenges include determining just what those best practices are (should you _always_ do background correction, is anti-backlash movement a requirement?) so the biologist doesn't have to be an automation or image processing expert, matching UI presentations to the mindset and vocabulary of the users, etc. There are lots of potential design choices in that process.

Kevin Ryan

On Sep 29, 2016 12:39, "Kathleen Pullin" <[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 started attending JavaScript meetups for help picking a framework for a game I'm writing (I just finished a code school bootcamp, and I'm writing a game, gee, ....)

At the meetups there were concepts that I explained from my background in microscopy (robotics and screen interactions, frequency distributions, 3D manipulators, lots of math), and the coders were interested in what is going on in the field. When asked to do a talk on programming in microscopy, I said, "Sure, put me down." Now I realize it's like I offered to talk about the history of Earth, and I'm trying to narrow it down to a one hour presentation on 4.5 billion years of geology, or maybe 3.5 billion of biology, or maybe the evolution of humans....

Does anyone have a suggestion for a specific topic on programming and microscopy of high relevancy to front end coders?

Thanks!

Kleo Pullin