Inspector Window Behavior

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Inspector Window Behavior

Chris O'Connell

I just updated to Micro-Manager 2.0.0-gamma1 20190609.  I noticed now when I click “Acquire” in the Multi-D window a new window opens with the data being acquired.    It seems that the auto stretch function on the histogram fails to function for the new window.  I configured inspector to use the top most window.

 

If I have a very dim image, with a 10 ms exposure for example, the displayed image in the capturing window is totally white and the auto stretch feature fails to function.  Maybe this is bug?

 

Chris O’Connell, PhD

Director, Advanced Light Microscopy Facility

 

University of Connecticut

Department of Physiology & Neurobiology

75 North Eagleville Road, U-3156

Storrs, CT 06269-3156

Office: 860-486-3271

[hidden email]

www.confocal.uconn.edu

 

 



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Re: Inspector Window Behavior

Stuurman, Nico
On 6/10/19 9:25 AM, O'Connell, Christopher wrote:

>
> I just updated to Micro-Manager 2.0.0-gamma1 20190609.  I noticed now
> when I click “Acquire” in the Multi-D window a new window opens with
> the data being acquired.    It seems that the auto stretch function on
> the histogram fails to function for the new window.  I configured
> inspector to use the top most window.
>
> If I have a very dim image, with a 10 ms exposure for example, the
> displayed image in the capturing window is totally white and the auto
> stretch feature fails to function.  Maybe this is bug?
>

That could be, but when I follow the same steps you describe, the
auto-stretch function works as expected.  Can you try to reproduce this
behavior with the demo camera, and describe every step to reproduce the
issue in detail?

Couple of things that come to mind:
- Does the histogram look correct?  If there is no histogram displayed,
click the gear icon in the top right corner of the Inspector Window and
make sure the Histogram update Rate is high enough
- Is it possible that your image is completeley saturated? What are the
Min, Max, and Avg values?
- Does manual adjustment of the triangle in the histogram make the image
visible?

Best,


Nico





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Re: Inspector Window Behavior

Chris O'Connell
Hi Nico.

This is a standard BPAE slide I am using, looking at the actin with a GFP filter set in epifluorescence with 60X oil immersion lens.  Camera is Prime 95B.  Here is the workflow:

1. Set Exposure to 10 ms.
2. Run live.  Histogram refresh is set to 5 Hz.  Min 148, Max 418.
3. Set Multi-D acquisition count to 1000, 0 ms interval.

When I click acquire, the window is initially completely white, and it is not responsive to auto or manual adjustments of the histogram.  When the acquisition is complete, the image appears in the window and histogram adjustment is functioning normally.  I just tried 20 ms and 100 ms exposure and those behave OK.  Not sure why 10 ms seems to have the problem.

Chris O'Connell, PhD
Director, Advanced Light Microscopy Facility

University of Connecticut
Department of Physiology & Neurobiology
75 North Eagleville Road, U-3156
Storrs, CT 06269-3156
Office: 860-486-3271
[hidden email]
www.confocal.uconn.edu



-----Original Message-----
From: Stuurman, Nico [mailto:[hidden email]]
Sent: Monday, June 10, 2019 7:35 PM
To: Micro-Manager General <[hidden email]>; O'Connell, Christopher <[hidden email]>
Subject: Re: [micro-manager-general] Inspector Window Behavior

On 6/10/19 9:25 AM, O'Connell, Christopher wrote:

>
> I just updated to Micro-Manager 2.0.0-gamma1 20190609.  I noticed now
> when I click "Acquire" in the Multi-D window a new window opens with
> the data being acquired.    It seems that the auto stretch function on
> the histogram fails to function for the new window.  I configured
> inspector to use the top most window.
>
> If I have a very dim image, with a 10 ms exposure for example, the
> displayed image in the capturing window is totally white and the auto
> stretch feature fails to function.  Maybe this is bug?
>

That could be, but when I follow the same steps you describe, the auto-stretch function works as expected.  Can you try to reproduce this behavior with the demo camera, and describe every step to reproduce the issue in detail?

Couple of things that come to mind:
- Does the histogram look correct?  If there is no histogram displayed, click the gear icon in the top right corner of the Inspector Window and make sure the Histogram update Rate is high enough
- Is it possible that your image is completeley saturated? What are the Min, Max, and Avg values?
- Does manual adjustment of the triangle in the histogram make the image visible?

Best,


Nico





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Re: Inspector Window Behavior

Stuurman, Nico

On 6/11/2019 6:42 AM, O'Connell, Christopher wrote:
> Camera is Prime 95B.  Here is the workflow:
>
> 1. Set Exposure to 10 ms.
> 2. Run live.  Histogram refresh is set to 5 Hz.  Min 148, Max 418.
> 3. Set Multi-D acquisition count to 1000, 0 ms interval.
>
> When I click acquire, the window is initially completely white, and it is not responsive to auto or manual adjustments of the histogram.  When the acquisition is complete, the image appears in the window and histogram adjustment is functioning normally.  I just tried 20 ms and 100 ms exposure and those behave OK.  Not sure why 10 ms seems to have the problem.

Ah!  100 fps at 1.4-2.6 MPixel (not sure which Prime95B you have)
results in 280-560 MB/sec of data to handle.  Quite a bit of work to do
for the code and making sure that no images get lost (which is the main
difference with live mode), handle metadata, etc...  Is this on a PC
with lots of RAM, and many cores?

There certainly is optimization to be done for high speed, large sized
cameras, but that is not something that I will be touching any time soon
(other things to do...). I did notice, however, that zoom level
sometimes has an effect on display (it is less work to display at 100%,
then to zoom in or out).  In the mean time, you at least get the data,
so this sounds like an annoyance rather than a show-stopper.

Best,


Nico





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Re: Inspector Window Behavior

Chris O'Connell
That makes sense.  At least I know what is causing it when we see that behavior.  Thanks!

Chris O’Connell, PhD
Director, Advanced Light Microscopy Facility

University of Connecticut
Department of Physiology & Neurobiology
75 North Eagleville Road, U-3156
Storrs, CT 06269-3156
Office: 860-486-3271
[hidden email]
www.confocal.uconn.edu




-----Original Message-----
From: Stuurman, Nico [mailto:[hidden email]]
Sent: Tuesday, June 11, 2019 12:06 PM
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] Inspector Window Behavior


On 6/11/2019 6:42 AM, O'Connell, Christopher wrote:
> Camera is Prime 95B.  Here is the workflow:
>
> 1. Set Exposure to 10 ms.
> 2. Run live.  Histogram refresh is set to 5 Hz.  Min 148, Max 418.
> 3. Set Multi-D acquisition count to 1000, 0 ms interval.
>
> When I click acquire, the window is initially completely white, and it is not responsive to auto or manual adjustments of the histogram.  When the acquisition is complete, the image appears in the window and histogram adjustment is functioning normally.  I just tried 20 ms and 100 ms exposure and those behave OK.  Not sure why 10 ms seems to have the problem.

Ah!  100 fps at 1.4-2.6 MPixel (not sure which Prime95B you have) results in 280-560 MB/sec of data to handle.  Quite a bit of work to do for the code and making sure that no images get lost (which is the main difference with live mode), handle metadata, etc...  Is this on a PC with lots of RAM, and many cores?

There certainly is optimization to be done for high speed, large sized cameras, but that is not something that I will be touching any time soon (other things to do...). I did notice, however, that zoom level sometimes has an effect on display (it is less work to display at 100%, then to zoom in or out).  In the mean time, you at least get the data, so this sounds like an annoyance rather than a show-stopper.

Best,


Nico





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Re: Inspector Window Behavior

mglotzer
It might be worth a quick test into whether this behavior is user profile
dependent. I reported a somewhat similar lack of responsiveness in image
updating last week that was connected to my user profile and rectified by
creating a new profile.



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Re: Inspector Window Behavior

MORRISON Harris
Hi,

When you say create a new user profile, do you mean the deleting the one one the hard drive or your establishments roaming profile? Here, if I have a problem with the profile on the hard disk , I can delete that one and when I log in next, my roaming profile is re-created.

Thanks and apologies if a daft question but we're having multiple issues with profile for certain users not being updated (Not remembering settings or exposures for the next login) and am now wondering if there is another file which records the user settings for MM 1.4 alone.

H


From: mglotzer <[hidden email]>
Sent: 12 June 2019 15:20
To: [hidden email]
Subject: Re: [micro-manager-general] Inspector Window Behavior
 
It might be worth a quick test into whether this behavior is user profile
dependent. I reported a somewhat similar lack of responsiveness in image
updating last week that was connected to my user profile and rectified by
creating a new profile.



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Re: Inspector Window Behavior

mglotzer
M-M 2.0 implements user profiles. Please see this link for more information:
micro-manager.org_wiki_Version_2.0_Profiles
<https://micro-manager.org/wiki/Version_2.0_Profiles>  

In micro-manager, you can simply create an additional profile.
Profile files on Windows are in
Users\currentUserName\AppData\Local\Micro-Manager though this folder and
files are hidden unless you change a setting to shown hidden files.

I think there are settings save for MM 1.4, but I don't know the details.

best,
Michael




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Re: Inspector Window Behavior

MORRISON Harris
Morning Michael,

Thanks for that and something to play with this morning......

Cheers,

Harris

From: mglotzer <[hidden email]>
Sent: 12 June 2019 19:07
To: [hidden email]
Subject: Re: [micro-manager-general] Inspector Window Behavior
 
M-M 2.0 implements user profiles. Please see this link for more information:
micro-manager.org_wiki_Version_2.0_Profiles
<https://micro-manager.org/wiki/Version_2.0_Profiles

In micro-manager, you can simply create an additional profile.
Profile files on Windows are in
Users\currentUserName\AppData\Local\Micro-Manager though this folder and
files are hidden unless you change a setting to shown hidden files.

I think there are settings save for MM 1.4, but I don't know the details.

best,
Michael




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