Two suggestions/requests for MicroManager

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Two suggestions/requests for MicroManager

Cammer, Michael

This is an awesome program but, of course, our lab has the following requests to improve it.

 

The exposure times entered in the Multi Dimensional Acquire window are propagated to the Live settings and this is a problem for us.  It would be great if these could be decoupled so for each setting (i.e. we have a green setting for using the 561 nm laser with certain emission filters) the live exposure time would be different than the acquire exposure time and would be remembered for each setting (e.g. 250 ms for live "Green" and 100 ms for live "Red" but 5000 ms for each acquisition).  This has become a problem where acquisition times are on the order of seconds but we like to preview at 250 ms exposures with the LUT cranked up.  

 

2.  In multi Dimensional Acquire do error checking for valid filenames.  One of our users got very frustrated the other evening that the software wasn't working. The next morning I looked over her shoulder to see how she was operating the instrument and the problem was simply that she had entered a filename something like "Ab 1:100 phalloidin" and my changing it to "Ab 1-100 phalloidin" fixed the problem.

 

Thanks and happy holidays!!

 

________________________________________________________

Michael Cammer, Assistant Research Scientist

Skirball Institute of Biomolecular Medicine

Lab: (212) 263-3208  Cell: (914) 309-3270

 


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Re: Two suggestions/requests for MicroManager

David Knecht
<base href="x-msg://792/">Hi Mike- I would have to disagree on the first one, as I was one who asked for them to be linked.  If you are playing with settings to figure out the correct exposure to use, it is nice when that exposure setting is propagated to the multi-D setup.  I often had problems the other way, that people would get the exposure figured out, set up the Multi-D and only after they started it realize that they were using the wrong exposure. I think that scenario is far more common than the one you describe.  Perhaps having a way to turn the linking off or on in prefs would help?  Dave

On Dec 19, 2012, at 11:12 AM, Cammer, Michael wrote:

This is an awesome program but, of course, our lab has the following requests to improve it.
 
The exposure times entered in the Multi Dimensional Acquire window are propagated to the Live settings and this is a problem for us.  It would be great if these could be decoupled so for each setting (i.e. we have a green setting for using the 561 nm laser with certain emission filters) the live exposure time would be different than the acquire exposure time and would be remembered for each setting (e.g. 250 ms for live "Green" and 100 ms for live "Red" but 5000 ms for each acquisition).  This has become a problem where acquisition times are on the order of seconds but we like to preview at 250 ms exposures with the LUT cranked up.  
 
2.  In multi Dimensional Acquire do error checking for valid filenames.  One of our users got very frustrated the other evening that the software wasn't working. The next morning I looked over her shoulder to see how she was operating the instrument and the problem was simply that she had entered a filename something like "Ab 1:100 phalloidin" and my changing it to "Ab 1-100 phalloidin" fixed the problem.
 
Thanks and happy holidays!!
 
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270
 
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Professor David Knecht    
Department of Molecular and Cell Biology
Microscopy Facility Director
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)




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Re: Two suggestions/requests for MicroManager

Cammer, Michael
Dear Dave et al,

The problem is that when there are long exposure times and people switch back to live mode to preview they think the instrument is hanging or photodamage their samples.

What about in a configuration definition such as this...

# Configuration presets
# Group: confocal
# Preset: blue
ConfigGroup,confocal,blue,LASER DTOL-Switch,Label,LASER 488
ConfigGroup,confocal,blue,LASER DTOL-Shutter,OnOff,0
ConfigGroup,confocal,blue,ASIFilterWheel_1,Label,ASI_525/50
ConfigGroup,confocal,blue,POWER DTOL-DAC-1,Volts,5.0000
ConfigGroup,confocal,blue,DA Z Stage,DA Device,PIEZO DTOL-DAC-0
ConfigGroup,confocal,blue,LudlShutter,State,0

...the following commands or similar ones were added?

ConfigGroup,confocal,blue,AcqExposure,ms,5000
ConfigGroup,confocal,blue,LiveExposure,ms,100
ConfigGroup,confocal,blue,AcqBinning,2,2
ConfigGroup,confocal,blue,LiveBinning,4,4

Absence of a definition or defined as -1 could have them coupled as you like.

Regards,

Michael

               
_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270

From: David Knecht [[hidden email]]
Sent: Wednesday, December 19, 2012 11:50 AM
To: Micro-Manager General
Subject: Re: [micro-manager-general] Two suggestions/requests for MicroManager

Hi Mike- I would have to disagree on the first one, as I was one who asked for them to be linked.  If you are playing with settings to figure out the correct exposure to use, it is nice when that exposure setting is propagated to the multi-D setup.  I often had problems the other way, that people would get the exposure figured out, set up the Multi-D and only after they started it realize that they were using the wrong exposure. I think that scenario is far more common than the one you describe.  Perhaps having a way to turn the linking off or on in prefs would help?  Dave

On Dec 19, 2012, at 11:12 AM, Cammer, Michael wrote:

This is an awesome program but, of course, our lab has the following requests to improve it.
 
The exposure times entered in the Multi Dimensional Acquire window are propagated to the Live settings and this is a problem for us.  It would be great if these could be decoupled so for each setting (i.e. we have a green setting for using the 561 nm laser with certain emission filters) the live exposure time would be different than the acquire exposure time and would be remembered for each setting (e.g. 250 ms for live "Green" and 100 ms for live "Red" but 5000 ms for each acquisition).  This has become a problem where acquisition times are on the order of seconds but we like to preview at 250 ms exposures with the LUT cranked up.  
 
2.  In multi Dimensional Acquire do error checking for valid filenames.  One of our users got very frustrated the other evening that the software wasn't working. The next morning I looked over her shoulder to see how she was operating the instrument and the problem was simply that she had entered a filename something like "Ab 1:100 phalloidin" and my changing it to "Ab 1-100 phalloidin" fixed the problem.
 
Thanks and happy holidays!!
 
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270
 
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Professor David Knecht    
Department of Molecular and Cell Biology
Microscopy Facility Director
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)




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Re: Two suggestions/requests for MicroManager

Sam Lord
In reply to this post by David Knecht
David Knecht wrote
Hi Mike- I would have to disagree on the first one, as I was one who asked for them to be linked.  If you are playing with settings to figure out the correct exposure to use, it is nice when that exposure setting is propagated to the multi-D setup.
OMG, I thought this was a bug and was about to report it. I'm really surprised that this is an intentional feature! :)

I think linking the Live exposure setting to the Multi-D exposure setting is very "dangerous" behavior, because it changes settings of the acquisition without warning. I've experienced several frustrating instances when I start a Multi-D run only to notice part-way through that the exposure times are not what they should be or what they were during the previous Multi-D run. I eventually realized what was happening, and that playing around with the exposure time in the Live window was propagating to the Multi-D settings without warning.

There are many times that I like to image in Live mode at a shorter exposure time---just enough to see the sample, but fast so that I can quickly focus and adjust the stage---then acquire real images at a significantly longer exposure time to get pretty, high signal/noise images. I think many people image in this manner. It is the standard approach in my lab, at least.

Being forced to not only check that all the exposure times in the Multi-D window are the same as before, but also *remember* what they were the last round, is not ideal. The Multi-D window can become quite complicated if you are including positions, time points, multiple colors, etc. I think that once you manually set an exposure time in the Multi-D window, it shouldn't change unless you manually change it. The convenience of having the Live exposure propagate to the Multi-D window only saves a few quick keystrokes a single time during an experiment. But if we have to readjust the Multi-D window every time we image Live at a shorter exposure time, that can be hundreds of keystrokes each day. Not to mention that, if you forget once, that run is different from the others and unusable.

The work around I currently use is to save the Multi-D acquisition settings, and reopen each time I start another imaging run. Certainly not an ideal work-around, as it is a lot of extra steps each run, but it ensures that I don't accidentally use the wrong exposure time and ruin a day's of experiments.

At minimum, I think this new "feature" should be able to be turned off, preferably by default. I know everyone has different preferences, but I don't think the default should be to automatically adjust settings that were manually inputted. Maybe a better solution would be a "Send to Multi-D" button next to the exposure time in the Live window. This would let David easily propagate to Multi-D when he wants, but wouldn't automatically link the two exposure times. Or a toggle button that would link and unlink Live with Multi-D.
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Re: Two suggestions/requests for MicroManager

David Knecht
Hi Sam- I am confused as to what you are describing, as I have not had that happen. Normally, I start in Live and determine the exposure I want.  Then I open Multi-D and set up the channel which takes the live setting for exposure.  Then I start the Multi-D.  If I went back to live, I would be using the same exposure.  When is it changing inappropriately?    Dave

On Dec 19, 2012, at 2:59 PM, Sam Lord wrote:

David Knecht wrote
Hi Mike- I would have to disagree on the first one, as I was one who asked
for them to be linked.  If you are playing with settings to figure out the
correct exposure to use, it is nice when that exposure setting is
propagated to the multi-D setup.

OMG, I thought this was a bug and was about to report it. I'm really
surprised that this is an intentional feature! :)

I think linking the Live exposure setting to the Multi-D exposure setting is
very "dangerous" behavior, because it changes settings of the acquisition
without warning. I've experienced several frustrating instances when I start
a Multi-D run only to notice part-way through that the exposure times are
not what they should be or what they were during the previous Multi-D run. I
eventually realized what was happening, and that playing around with the
exposure time in the Live window was propagating to the Multi-D settings
without warning.

There are many times that I like to image in Live mode at a shorter exposure
time---just enough to see the sample, but fast so that I can quickly focus
and adjust the stage---then acquire real images at a significantly longer
exposure time to get pretty, high signal/noise images. I think many people
image in this manner. It is the standard approach in my lab, at least.

Being forced to not only check that all the exposure times in the Multi-D
window are the same as before, but also *remember* what they were the last
round, is not ideal. The Multi-D window can become quite complicated if you
are including positions, time points, multiple colors, etc. I think that
once you manually set an exposure time in the Multi-D window, it shouldn't
change unless you manually change it. The convenience of having the Live
exposure propagate to the Multi-D window only saves a few quick keystrokes a
single time during an experiment. But if we have to readjust the Multi-D
window every time we image Live at a shorter exposure time, that can be
hundreds of keystrokes each day. Not to mention that, if you forget once,
that run is different from the others and unusable.

The work around I currently use is to save the Multi-D acquisition settings,
and reopen each time I start another imaging run. Certainly not an ideal
work-around, as it is a lot of extra steps each run, but it ensures that I
don't accidentally use the wrong exposure time and ruin a day's of
experiments.

At minimum, I think this new "feature" should be able to be turned off,
preferably by default. I know everyone has different preferences, but I
don't think the default should be to automatically adjust settings that were
manually inputted. Maybe a better solution would be a "Send to Multi-D"
button next to the exposure time in the Live window. This would let David
easily propagate to Multi-D when he wants, but wouldn't automatically link
the two exposure times. Or a toggle button that would link and unlink Live
with Multi-D.



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View this message in context: http://micro-manager.3463995.n2.nabble.com/Two-suggestions-requests-for-MicroManager-tp7579139p7579144.html
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Professor David Knecht    
Department of Molecular and Cell Biology
Microscopy Facility Director
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)




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Re: Two suggestions/requests for MicroManager

Sam Lord
David Knecht wrote
I am confused as to what you are describing, as I have not had that happen. Normally, I start in Live and determine the exposure I want.  Then I open Multi-D and set up the channel which takes the live setting for exposure.  Then I start the Multi-D.  If I went back to live, I would be using the same exposure.  When is it changing inappropriately?
If I have two channels in the Multi-D acquisition window with manually set exposure times, let's say Cy5 and DAPI with 100 ms each. Then I go to the Live window and select Cy5, change the exposure time in the Live window to 22 ms, then click the "Live" button. The exposure time in the Multi-D acquisition is now 22 ms for Cy5.
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Re: Two suggestions/requests for MicroManager

Nico Stuurman-2
Hi Sam and David,

Great discussion!  Very helpful to get your input.  

I add an option (unchecked by default) to couple the exposure times in the Main and MDA windows.  What may be a bit confusing is that the Main window will remember the exposure times associated with a configuration preset, but only for the current channelgroup (which is something that you set in the MDA window).  Hope this will work nicely and intuitively for everyone, otherwise, please let us know.  This change will be in tonight's build.

Best,

Nico

On Dec 19, 2012, at 3:20 PM, Sam Lord wrote:

> David Knecht wrote
>> I am confused as to what you are describing, as I have not had that
>> happen. Normally, I start in Live and determine the exposure I want.  Then
>> I open Multi-D and set up the channel which takes the live setting for
>> exposure.  Then I start the Multi-D.  If I went back to live, I would be
>> using the same exposure.  When is it changing inappropriately?
>
> If I have two channels in the Multi-D acquisition window with manually set
> exposure times, let's say Cy5 and DAPI with 100 ms each. Then I go to the
> Live window and select Cy5, change the exposure time in the Live window to
> 22 ms, then click the "Live" button. The exposure time in the Multi-D
> acquisition is now 22 ms for Cy5.
>


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Re: Two suggestions/requests for MicroManager

Cammer, Michael
Thank you!  We'll try within the next week or so.
Regards,
Michael

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270

________________________________________
From: Nico Stuurman [[hidden email]]
Sent: Sunday, December 23, 2012 9:05 PM
To: Micro-Manager General
Subject: Re: [micro-manager-general] Two suggestions/requests for MicroManager

Hi Sam and David,

Great discussion!  Very helpful to get your input.

I add an option (unchecked by default) to couple the exposure times in the Main and MDA windows.  What may be a bit confusing is that the Main window will remember the exposure times associated with a configuration preset, but only for the current channelgroup (which is something that you set in the MDA window).  Hope this will work nicely and intuitively for everyone, otherwise, please let us know.  This change will be in tonight's build.

Best,

Nico

On Dec 19, 2012, at 3:20 PM, Sam Lord wrote:

> David Knecht wrote
>> I am confused as to what you are describing, as I have not had that
>> happen. Normally, I start in Live and determine the exposure I want.  Then
>> I open Multi-D and set up the channel which takes the live setting for
>> exposure.  Then I start the Multi-D.  If I went back to live, I would be
>> using the same exposure.  When is it changing inappropriately?
>
> If I have two channels in the Multi-D acquisition window with manually set
> exposure times, let's say Cy5 and DAPI with 100 ms each. Then I go to the
> Live window and select Cy5, change the exposure time in the Live window to
> 22 ms, then click the "Live" button. The exposure time in the Multi-D
> acquisition is now 22 ms for Cy5.
>


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Re: Two suggestions/requests for MicroManager

Sam Lord
In reply to this post by Nico Stuurman-2
Nico Stuurman-2 wrote
I add an option (unchecked by default) to couple the exposure times in the Main and MDA windows.  What may be a bit confusing is that the Main window will remember the exposure times associated with a configuration preset, but only for the current channelgroup (which is something that you set in the MDA window).
Thanks, Nico. I look forward to trying this in the New Year!

-Sam