PointGrey Color Mode Imagesnap Fails in MM2 gamma

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PointGrey Color Mode Imagesnap Fails in MM2 gamma

Peter Braubach

Hi all,

 

When trying to capture an image in MM 2.0.0 gamma1 (20180803) with an point grey GS3 camera in 32bit color mode no image is returned. There is an image in live mode.

There are some errors in the core log which I do not understand: 2018-08-04T12:57:43.006580 tid13044 [IFO,App] java.lang.IllegalArgumentException

(full core log of this session https://pastebin.com/pAsrEEAw).

 

In MM 2.0.0 beta (beta3 20180120) image capture, live mode and mda works fine in 32bit color mode.

(core log https://pastebin.com/Qqv0Jd8U).

 

Does somebody know how to approach this issue? Can I be of any help.

 

Kind regards

Peter


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Re: PointGrey Color Mode Imagesnap Fails in MM2 gamma

Stuurman, Nico
Hi Peter,

> When trying to capture an image in MM 2.0.0 gamma1 (20180803) with an
> point grey GS3 camera in 32bit color mode no image is returned. There
> is an image in live mode.
>
> There are some errors in the core log which I do not understand:
> 2018-08-04T12:57:43.006580 tid13044 [IFO,App]
> java.lang.IllegalArgumentException
>
> (full core log of this session https://pastebin.com/pAsrEEAw 
> <https://pastebin.com/pAsrEEAw>).
>

Try unchecking "Mouse Moves Stage" in the "Tools" menu, and let us know
if that solved the problem.

If you do want to use "Mouse Moves Stage", make sure to update/set the
pixel size configuration.

This particular situation is certainly not handled nicely by the code,
and I'll have a look at it.

Best,


Nico


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Re: PointGrey Color Mode Imagesnap Fails in MM2 gamma

Stuurman, Nico
On 8/13/18 12:15 PM, Nico Stuurman wrote:

> Hi Peter,
>
>> When trying to capture an image in MM 2.0.0 gamma1 (20180803) with an
>> point grey GS3 camera in 32bit color mode no image is returned. There
>> is an image in live mode.
>>
>> There are some errors in the core log which I do not understand:
>> 2018-08-04T12:57:43.006580 tid13044 [IFO,App]
>> java.lang.IllegalArgumentException
>>
>> (full core log of this session https://pastebin.com/pAsrEEAw 
>> <https://pastebin.com/pAsrEEAw>).
>>
>
> Try unchecking "Mouse Moves Stage" in the "Tools" menu, and let us
> know if that solved the problem.
>
> If you do want to use "Mouse Moves Stage", make sure to update/set the
> pixel size configuration.
>
> This particular situation is certainly not handled nicely by the code,
> and I'll have a look at it.

Also, there seem to be quite a few unresolved issues with RGB in 2.0
gamma.  I will have a bit of a look at it, but it does not have high
priority for me.

Best,


Nico



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Re: PointGrey Color Mode Imagesnap Fails in MM2 gamma

Peter Braubach
In reply to this post by Stuurman, Nico
Hi Nico,

 thank you for your reply.

I unchecked the "mouse moves stage" option and the camera still does not capture an image in multid or when using snap image/image to collection.

In one case I could save an image, however I fail to replicate the situation. I will try to do so again tomorrow and will also save logs.
Further MM crashed to desktop while changing the pixel mode to 32bit rgb.

Kind regards
Peter
--
Dr. med. Peter Braubach
Koordinator Lungengewebebank
Arbeitsgruppe Lungenforschung

Institut für Pathologie
Medizinische Hochschule Hannover
OE 5110, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
Tel.: +49 511 532-8494
[hidden email]
www.mh-hannover.de
 

-----Original Message-----
From: Nico Stuurman <[hidden email]>
Sent: 13 August 2018 21:15
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] PointGrey Color Mode Imagesnap Fails in MM2 gamma

Hi Peter,

> When trying to capture an image in MM 2.0.0 gamma1 (20180803) with an
> point grey GS3 camera in 32bit color mode no image is returned. There
> is an image in live mode.
>
> There are some errors in the core log which I do not understand:
> 2018-08-04T12:57:43.006580 tid13044 [IFO,App]
> java.lang.IllegalArgumentException
>
> (full core log of this session https://pastebin.com/pAsrEEAw 
> <https://pastebin.com/pAsrEEAw>).
>

Try unchecking "Mouse Moves Stage" in the "Tools" menu, and let us know if that solved the problem.

If you do want to use "Mouse Moves Stage", make sure to update/set the pixel size configuration.

This particular situation is certainly not handled nicely by the code, and I'll have a look at it.

Best,


Nico


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Re: PointGrey Color Mode Imagesnap Fails in MM2 gamma

Peter Braubach
Hi Nico,

 Please excuse the delay in my response. I was held up all week.
I could not reproduce the conditions under which I (thought) I successfully captured an color image in gamma.

I tried several conditions, including your "mouse moves stage" suggestion (see below). However I cannot save color images in gamma.

Thank you for your effort. I know that color imaging is no priority and appreciate that you are looking into it anyway.

Since I have started with MM I have learned a lot about microscopes, programming, system integration and much more. A big thank you to you and the whole micro-manager devs and people on the ML.

Peter

PS: is there any way to do white balancing in MM?

Conditions, Logs
0. OpenMM -> Live -> To Album -> CloseMM
Successful capture of grayscale image
Log: https://pastebin.com/n1KW6eY1

1. OpenMM -> 32Bit RGB Mode -> Live -> To Album -> CloseMM
Empty image, inspector shows "No Data"
Log: https://pastebin.com/s6t6xhxZ

2. OpenMM -> turn off "mouse moves stage" -> Live -> To Album -> CloseMM
Empty image like in 1.
Log: https://pastebin.com/PVX53fWY

Also toggeling mouse moves stage on/off/on etc. does not do anything.

3. OpenMM -> Live -> 32BitRGB -> Crash to desktop
When changing the pixel type in live mode MM crashes to desktop without any warning or error.
Log: https://pastebin.com/eRcq8hYz

Config used in all the examples: https://pastebin.com/1RqLdXRJ


-----Original Message-----
From: [hidden email] <[hidden email]>
Sent: 14 August 2018 20:24
To: [hidden email]
Subject: Re: [micro-manager-general] PointGrey Color Mode Imagesnap Fails in MM2 gamma

Hi Nico,

 thank you for your reply.

I unchecked the "mouse moves stage" option and the camera still does not capture an image in multid or when using snap image/image to collection.

In one case I could save an image, however I fail to replicate the situation. I will try to do so again tomorrow and will also save logs.
Further MM crashed to desktop while changing the pixel mode to 32bit rgb.

Kind regards
Peter
--
Dr. med. Peter Braubach
Koordinator Lungengewebebank
Arbeitsgruppe Lungenforschung

Institut für Pathologie
Medizinische Hochschule Hannover
OE 5110, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
Tel.: +49 511 532-8494
[hidden email]
www.mh-hannover.de
 

-----Original Message-----
From: Nico Stuurman <[hidden email]>
Sent: 13 August 2018 21:15
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] PointGrey Color Mode Imagesnap Fails in MM2 gamma

Hi Peter,

> When trying to capture an image in MM 2.0.0 gamma1 (20180803) with an
> point grey GS3 camera in 32bit color mode no image is returned. There
> is an image in live mode.
>
> There are some errors in the core log which I do not understand:
> 2018-08-04T12:57:43.006580 tid13044 [IFO,App]
> java.lang.IllegalArgumentException
>
> (full core log of this session https://pastebin.com/pAsrEEAw 
> <https://pastebin.com/pAsrEEAw>).
>

Try unchecking "Mouse Moves Stage" in the "Tools" menu, and let us know if that solved the problem.

If you do want to use "Mouse Moves Stage", make sure to update/set the pixel size configuration.

This particular situation is certainly not handled nicely by the code, and I'll have a look at it.

Best,


Nico


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Re: PointGrey Color Mode Imagesnap Fails in MM2 gamma

Stuurman, Nico
Hi Peter,

> I could not reproduce the conditions under which I (thought) I successfully captured an color image in gamma.
>
> I tried several conditions, including your "mouse moves stage" suggestion (see below). However I cannot save color images in gamma.

I started a branch on github
(https://github.com/nicost/micro-manager/tree/ColorDisplay) to get RGB
images working in gamma.  I made quite some progress (including correct
brightness/contrast controls), but found that the democamera only
displays red and green.  It turns out that the democamera RGB mode
produces images as BGRA wheres ImageJ appears to work with the ARGB
color model (despite comments to the contrary in the DemoCamera source
code), so I think that explains why I see only 2 colors with the
DemoCamera.  I do not have an RGB Point Grey camera to check.

I asked Mark if he knows what is going on and how to proceed, but I have
not heard from him for a while.  Hopefully he'll respond soon.

Best,

Nico




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Re: PointGrey Color Mode Imagesnap Fails in MM2 gamma

Stuurman, Nico
In reply to this post by Peter Braubach
Hi Peter,

>   Please excuse the delay in my response. I was held up all week.
> I could not reproduce the conditions under which I (thought) I successfully captured an color image in gamma.
>
> I tried several conditions, including your "mouse moves stage" suggestion (see below). However I cannot save color images in gamma.
>
> Thank you for your effort. I know that color imaging is no priority and appreciate that you are looking into it anyway.

I just tested the latest version of 2.0 gamma with a Blackfly
(BFLY-U3-23S6C-C) and color mode seems to work fine (bit hard to test
the color correctness, since I forgot to bring a lens).  Only problem I
detected is that changing pixeltype from RGB to 16bit while live mode is
running causes a crash.  The DemoCamera does not even allow this change,
and the simplest fix will be to disallow it in the PG adapter as well. 
Till then, just don't do it.

Let me know how your camera behaves with the latest build of gamma.

Best,

Nico


>
> Since I have started with MM I have learned a lot about microscopes, programming, system integration and much more. A big thank you to you and the whole micro-manager devs and people on the ML.
>
> Peter
>
> PS: is there any way to do white balancing in MM?
>
> Conditions, Logs
> 0. OpenMM -> Live -> To Album -> CloseMM
> Successful capture of grayscale image
> Log: https://pastebin.com/n1KW6eY1
>
> 1. OpenMM -> 32Bit RGB Mode -> Live -> To Album -> CloseMM
> Empty image, inspector shows "No Data"
> Log: https://pastebin.com/s6t6xhxZ
>
> 2. OpenMM -> turn off "mouse moves stage" -> Live -> To Album -> CloseMM
> Empty image like in 1.
> Log: https://pastebin.com/PVX53fWY
>
> Also toggeling mouse moves stage on/off/on etc. does not do anything.
>
> 3. OpenMM -> Live -> 32BitRGB -> Crash to desktop
> When changing the pixel type in live mode MM crashes to desktop without any warning or error.
> Log: https://pastebin.com/eRcq8hYz
>
> Config used in all the examples: https://pastebin.com/1RqLdXRJ
>
>
> -----Original Message-----
> From: [hidden email] <[hidden email]>
> Sent: 14 August 2018 20:24
> To: [hidden email]
> Subject: Re: [micro-manager-general] PointGrey Color Mode Imagesnap Fails in MM2 gamma
>
> Hi Nico,
>
>   thank you for your reply.
>
> I unchecked the "mouse moves stage" option and the camera still does not capture an image in multid or when using snap image/image to collection.
>
> In one case I could save an image, however I fail to replicate the situation. I will try to do so again tomorrow and will also save logs.
> Further MM crashed to desktop while changing the pixel mode to 32bit rgb.
>
> Kind regards
> Peter
> --
> Dr. med. Peter Braubach
> Koordinator Lungengewebebank
> Arbeitsgruppe Lungenforschung
>
> Institut für Pathologie
> Medizinische Hochschule Hannover
> OE 5110, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
> Tel.: +49 511 532-8494
> [hidden email]
> www.mh-hannover.de
>  
>
> -----Original Message-----
> From: Nico Stuurman <[hidden email]>
> Sent: 13 August 2018 21:15
> To: Micro-Manager General <[hidden email]>
> Subject: Re: [micro-manager-general] PointGrey Color Mode Imagesnap Fails in MM2 gamma
>
> Hi Peter,
>
>> When trying to capture an image in MM 2.0.0 gamma1 (20180803) with an
>> point grey GS3 camera in 32bit color mode no image is returned. There
>> is an image in live mode.
>>
>> There are some errors in the core log which I do not understand:
>> 2018-08-04T12:57:43.006580 tid13044 [IFO,App]
>> java.lang.IllegalArgumentException
>>
>> (full core log of this session https://pastebin.com/pAsrEEAw
>> <https://pastebin.com/pAsrEEAw>).
>>
> Try unchecking "Mouse Moves Stage" in the "Tools" menu, and let us know if that solved the problem.
>
> If you do want to use "Mouse Moves Stage", make sure to update/set the pixel size configuration.
>
> This particular situation is certainly not handled nicely by the code, and I'll have a look at it.
>
> Best,
>
>
> Nico
>
>
> ------------------------------------------------------------------------------
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>


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Re: PointGrey Color Mode Imagesnap Fails in MM2 gamma

Stuurman, Nico

> Hi Nico,
>
>
> Thank you for your quick update. I tested the current nightly (20180824) and single image capture in 32BitRGB mode works.
>
> What does not work is multi-D. When doing this the last image is saved in every step and there are some errors in the log.

You must be saving as single TIFFs. Try saving as multi-page TIFFS instead.

The next nightly build should save in single TIFFs correctly, however,
something goes wrong reading them (which also results in the lack of
display in an ongoing acquisition).

> I am not 100% happy with the color rendition, however I am not sure what is hardware and software. I can correct some of it out, but not fully. A simple white balance does not help. The halogen lamp is a bit old and getting more orange than I like it. Maybe I have to get a new one soon.

There are no facilities for color correction (setting a white point). 
This is best accomplished at the level of the hardware itself, and some
cameras have facilities to do this.  You may be better off using 1.4 or
beta, where you can set the intensity of each color (RGB) individually,
hence adjust the color balance, however,  don't think that will result
in a nice/easy workflow.

Best,

Nico

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