album help

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album help

tsuchyna

Hello Community,

 

I have been trying to use the album function to collect a images in brightfield and fluorescence.

 

MM beta:

·         Always opens a new window as I switch filter sets between brightfield and fluorescence.

 

MM gamma:

·         This program works – sends new images to one album window - when I switch between filter sets only when taking single frame images

·         However, when I activate the On-the-Fly processor “Frame combiner”, the album window opens with no image - saying “waiting for image” - and no image ever appears.

·         The live window keeps showing realtime images.

 

Has anyone ever had problems with the album function opening multiple album windows, or the frame combiner and not been able to get an image to appear?

 

I’m using latest versions of MM beta and gamma, Windows 7 operating system and latest version of Java 8.

 

Thanks

 

Tom

 

Thomas M. Suchyna, Ph.D.

Dept. of Physiology and Biophysics

301 Cary Hall

SUNY at Buffalo

Buffalo, NY 14214

Phone: 716-829-5156

e-mail: [hidden email]

 



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Re: album help

Nico Stuurman-2
Hi Tom,

> I have been trying to use the album function to collect a images in
> brightfield and fluorescence.
>
> MM beta:
>
> ·Always opens a new window as I switch filter sets between brightfield
> and fluorescence.
>

Don't use beta.  It is unsupported, unmaintained, etc..  Downloads are
there only for historical reasons

> MM gamma:
>
> ·This program works – sends new images to one album window - when I
> switch between filter sets */only when taking single frame images/*
>
> ·However, when I activate the On-the-Fly processor “Frame combiner”,
> the album window opens with no image - saying “waiting for image” -
> and no image ever appears.
>
> ·The live window keeps showing realtime images.
>

That is an interesting use case!  I looked at the code, and the function
adding the image to the album sends the image through the On-the-Fly
processor pipeline.  Worse, it starts a new pipeline for each image, so
there is no way that multiple images can ever make it through the same
pipeline for the Frame combiner to produce an output.

That behavior is not what I would expect when pressing the Album button
in the Snap/Live window (it is the behavior I would expect when pressing
the Album button in the main window, which first snaps a new image). 
There is n easy fix without changing the API of Micro-Manager.  I'll
talk to the API designer (Mark Tsuchida) and propose extend the API to
make it possible to add images to an album without sending them through
the processing pipeline.

Best,


Nico





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Re: album help

tsuchyna
Hi Nico,

Thanks for the quick reply and remedy. Hope its workable.

Tom

-----Original Message-----
From: Nico Stuurman [mailto:[hidden email]]
Sent: Tuesday, January 14, 2020 1:23 PM
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] album help

Hi Tom,

> I have been trying to use the album function to collect a images in
> brightfield and fluorescence.
>
> MM beta:
>
> ·Always opens a new window as I switch filter sets between brightfield
> and fluorescence.
>

Don't use beta.  It is unsupported, unmaintained, etc..  Downloads are there only for historical reasons

> MM gamma:
>
> ·This program works - sends new images to one album window - when I
> switch between filter sets */only when taking single frame images/*
>
> ·However, when I activate the On-the-Fly processor "Frame combiner",
> the album window opens with no image - saying "waiting for image" -
> and no image ever appears.
>
> ·The live window keeps showing realtime images.
>

That is an interesting use case!  I looked at the code, and the function adding the image to the album sends the image through the On-the-Fly processor pipeline.  Worse, it starts a new pipeline for each image, so there is no way that multiple images can ever make it through the same pipeline for the Frame combiner to produce an output.

That behavior is not what I would expect when pressing the Album button in the Snap/Live window (it is the behavior I would expect when pressing the Album button in the main window, which first snaps a new image). There is n easy fix without changing the API of Micro-Manager.  I'll talk to the API designer (Mark Tsuchida) and propose extend the API to make it possible to add images to an album without sending them through the processing pipeline.

Best,


Nico





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Re: album help

Nico Stuurman-2
Hi Tom,

For now, I decided to have the Album use the "Default" rather than the
"Snap/Live" pipeline.  So, by unchecking the "Default" pipeline, and
checking the Snap/Live Pipeline, you can now use the FrameCombiner in
the Live window, and clicking the Album button in the Live Window to
transfer the latest image in the viewer to the Album without going
through the pipeline again.

This is a bit of a hack, but all I can come up with without changing the
API.  It should be in tomorrow's build of 2.0-gamma.

>> I have been trying to use the album function to collect a images in
>> brightfield and fluorescence.
>>
>>   when I activate the On-the-Fly processor "Frame combiner",
>> the album window opens with no image - saying "waiting for image" -
>> and no image ever appears.
>>
>> ·The live window keeps showing realtime images.
>>
> That is an interesting use case!  I looked at the code, and the function adding the image to the album sends the image through the On-the-Fly processor pipeline.  Worse, it starts a new pipeline for each image, so there is no way that multiple images can ever make it through the same pipeline for the Frame combiner to produce an output.
>
> That behavior is not what I would expect when pressing the Album button in the Snap/Live window (it is the behavior I would expect when pressing the Album button in the main window, which first snaps a new image). There is n easy fix without changing the API of Micro-Manager.  I'll talk to the API designer (Mark Tsuchida) and propose extend the API to make it possible to add images to an album without sending them through the processing pipeline.



Best,

Nico


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Re: album help

tsuchyna
Thanks Nico. I will give that a try and let you know.

Tom

-----Original Message-----
From: Nico Stuurman [mailto:[hidden email]]
Sent: Wednesday, January 15, 2020 11:22 PM
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] album help

Hi Tom,

For now, I decided to have the Album use the "Default" rather than the "Snap/Live" pipeline.  So, by unchecking the "Default" pipeline, and checking the Snap/Live Pipeline, you can now use the FrameCombiner in the Live window, and clicking the Album button in the Live Window to transfer the latest image in the viewer to the Album without going through the pipeline again.

This is a bit of a hack, but all I can come up with without changing the API.  It should be in tomorrow's build of 2.0-gamma.

>> I have been trying to use the album function to collect a images in
>> brightfield and fluorescence.
>>
>>   when I activate the On-the-Fly processor "Frame combiner", the
>> album window opens with no image - saying "waiting for image" - and
>> no image ever appears.
>>
>> ·The live window keeps showing realtime images.
>>
> That is an interesting use case!  I looked at the code, and the function adding the image to the album sends the image through the On-the-Fly processor pipeline.  Worse, it starts a new pipeline for each image, so there is no way that multiple images can ever make it through the same pipeline for the Frame combiner to produce an output.
>
> That behavior is not what I would expect when pressing the Album button in the Snap/Live window (it is the behavior I would expect when pressing the Album button in the main window, which first snaps a new image). There is n easy fix without changing the API of Micro-Manager.  I'll talk to the API designer (Mark Tsuchida) and propose extend the API to make it possible to add images to an album without sending them through the processing pipeline.



Best,

Nico


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[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

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