Black screen/white screen

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Black screen/white screen

Knecht, David
One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave


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Re: [micro-manager-general] Black screen/white screen

Hoover, Karl
Hello David,

Could you describe the precise conditions under which you see this image 'reversal.' Of course, our intention is that black is 0 and and white is all bits on. Please tell us image size, mode, # bits etc.

Best Regards,
Karl Hoover

________________________________________
From: Knecht, David [[hidden email]]
Sent: Monday, January 25, 2010 14:25
To: Micro-Manager General
Subject: [micro-manager-general] Black screen/white screen

One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave


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Re: [micro-manager-general] Black screen/white screen

Knecht, David
I happened to be in 8 bit mode, bin 2x (about 600x600), 125ms exposure but I don't think it matters.  I will do more testing tomorrow when I am in the lab to get specifics.  It happens when the gain or integration time is too long so that the entire image is saturated.  The student thinks there is too little light when in fact there is too much.  As you turn the light or integration time down, it switches from black to gray levels.  Dave

On Jan 25, 2010, at 5:33 PM, Hoover, Karl wrote:

> Hello David,
>
> Could you describe the precise conditions under which you see this image 'reversal.' Of course, our intention is that black is 0 and and white is all bits on. Please tell us image size, mode, # bits etc.
>
> Best Regards,
> Karl Hoover
>
> ________________________________________
> From: Knecht, David [[hidden email]]
> Sent: Monday, January 25, 2010 14:25
> To: Micro-Manager General
> Subject: [micro-manager-general] Black screen/white screen
>
> One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave
>
>
> ------------------------------------------------------------------------------
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Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)



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Re: [micro-manager-general] Black screen/white screen

Shalin Mehta
In reply to this post by Hoover, Karl
Hi Karl and David,

 I have noticed this also. However it is a 'feature' and not a 'bug'. It happens when we select 'Auto-stretch' for the look up table. When the whole image is saturated, all pixels are 255 - the entire LUT is stretched (or rather squeezed) to 255. When Auto-stretch is not used, and the user selects the histogram axis that maps to LUT, this does not happen.

best
Shalin

mobile: +65-90694182
blog: shalin.wordpress.com

Bioimaging Lab, Block-E3A, #7-10                
Div of Bioengineering, NUS Singapore 117574  
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/people.asp#shalinm


On Tue, Jan 26, 2010 at 6:33 AM, Hoover, Karl <[hidden email]> wrote:
Hello David,

Could you describe the precise conditions under which you see this image 'reversal.' Of course, our intention is that black is 0 and and white is all bits on. Please tell us image size, mode, # bits etc.

Best Regards,
Karl Hoover

________________________________________
From: Knecht, David [[hidden email]]
Sent: Monday, January 25, 2010 14:25
To: Micro-Manager General
Subject: [micro-manager-general] Black screen/white screen

One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave


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Re: [micro-manager-general] Black screen/white screen

Julien Husson-3
In reply to this post by Knecht, David
Hi David and Karl,
if I may : I also see this saturation as a black level, though I think I also
saw the situation where it saturates in white. I intuitively thought it was
related to the histogram autostretch, but that's just a guess.
Best,
Julien

On Mon, 25 Jan 2010 20:24:59 -0500, David Knecht wrote

> I happened to be in 8 bit mode, bin 2x (about 600x600), 125ms
> exposure but I don't think it matters.  I will do more testing
> tomorrow when I am in the lab to get specifics.  It happens when the
> gain or integration time is too long so that the entire image is
> saturated.  The student thinks there is too little light when in
> fact there is too much.  As you turn the light or integration time
> down, it switches from black to gray levels.  Dave
>
> On Jan 25, 2010, at 5:33 PM, Hoover, Karl wrote:
>
> > Hello David,
> >
> > Could you describe the precise conditions under which you see this image
'reversal.' Of course, our intention is that black is 0 and and white is all
bits on. Please tell us image size, mode, # bits etc.

> >
> > Best Regards,
> > Karl Hoover
> >
> > ________________________________________
> > From: Knecht, David [[hidden email]]
> > Sent: Monday, January 25, 2010 14:25
> > To: Micro-Manager General
> > Subject: [micro-manager-general] Black screen/white screen
> >
> > One of the things that I find most challenging in teaching with
Micro-manager is that when the image is saturated, it shows as a black screen
with values of 255.  This is really confusing to the novice when we train them
to recognize black as 0 and 255 as white.  Why is this happening and is there
anything I can do to prevent it?  Dave

> >
> >
> > ------------------------------------------------------------------------------
> > The Planet: dedicated and managed hosting, cloud storage, colocation
> > Stay online with enterprise data centers and the best network in the business
> > Choose flexible plans and management services without long-term contracts
> > Personal 24x7 support from experience hosting pros just a phone call away.
> > http://p.sf.net/sfu/theplanet-com
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> > micro-manager-general mailing list
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> > https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >
> > ------------------------------------------------------------------------------
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> > Choose flexible plans and management services without long-term contracts
> > Personal 24x7 support from experience hosting pros just a phone call away.
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> > _______________________________________________
> > micro-manager-general mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
> Dr. David Knecht    
> Department of Molecular and Cell Biology
> Co-head Flow Cytometry and Confocal Microscopy Facility
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the
> business Choose flexible plans and management services without long-
> term contracts Personal 24x7 support from experience hosting pros
> just a phone call away. http://p.sf.net/sfu/theplanet-com
_______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general


--
Julien Husson, postdoc
Macromolécules et Microsystèmes en Biologie et en Médecine
Laboratoire Physico Chimie Curie - UMR 168
Institut Curie
11 rue P. et M. Curie, 75231 PARIS Cedex 05, FRANCE
Tel : (33) (0) 1 56 24 67 75
Fax : (33) (0) 1 40 51 06 36
http://www.curie.fr/equipe/69/lang/_gb


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Re: [micro-manager-general] Black screen/white screen

Julien Husson-3
In reply to this post by Shalin Mehta
Sorry didn't see this post when writing...
Best
On Tue, 26 Jan 2010 09:56:03 +0800, Shalin Mehta wrote
> Hi Karl and David,
>
>  I have noticed this also. However it is a 'feature' and not a 'bug'. It happens when we select 'Auto-stretch' for the look up table. When the whole image is saturated, all pixels are 255 - the entire LUT is stretched (or rather squeezed) to 255. When Auto-stretch is not used, and the user selects the histogram axis that maps to LUT, this does not happen.
>
> best
Shalin

>
> mobile: +65-90694182
> blog: shalin.wordpress.com
>
> Bioimaging Lab, Block-E3A, #7-10                
> Div of Bioengineering, NUS Singapore 117574  
> website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/people.asp#shalinm
>
> On Tue, Jan 26, 2010 at 6:33 AM, Hoover, Karl <[hidden email]> wrote:
>
Hello David,
>
> Could you describe the precise conditions under which you see this image 'reversal.' Of course, our intention is that black is 0 and and white is all bits on. Please tell us image size, mode, # bits etc.
>
> Best Regards,
> Karl Hoover
>
> ________________________________________
> From: Knecht, David [[hidden email]]
>
> Sent: Monday, January 25, 2010 14:25
> To: Micro-Manager General
> Subject: [micro-manager-general] Black screen/white screen
>
> One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
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> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
> ------------------------------------------------------------------------------
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> Stay online with enterprise data centers and the best network in the business
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> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>


--
Julien Husson, postdoc
Macromolécules et Microsystèmes en Biologie et en Médecine
Laboratoire Physico Chimie Curie - UMR 168
Institut Curie
11 rue P. et M. Curie, 75231 PARIS Cedex 05, FRANCE
Tel : (33) (0) 1 56 24 67 75
Fax : (33) (0) 1 40 51 06 36
http://www.curie.fr/equipe/69/lang/_gb

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Re: [micro-manager-general] Black screen/white screen

Hoover, Karl
In reply to this post by Shalin Mehta
Shalin,
Exactly correct this display happens only if auto-stretching is on. So, in your opinion as a knowledgeable user, is the behavior correct, or perhaps the histogram should be 'stretched ' in the other direction?

Best Regards,
Karl Hoover
________________________________________
From: Shalin Mehta [[hidden email]]
Sent: Monday, January 25, 2010 17:56
To: Micro-Manager General
Subject: Re: [micro-manager-general] Black screen/white screen

Hi Karl and David,

 I have noticed this also. However it is a 'feature' and not a 'bug'. It happens when we select 'Auto-stretch' for the look up table. When the whole image is saturated, all pixels are 255 - the entire LUT is stretched (or rather squeezed) to 255. When Auto-stretch is not used, and the user selects the histogram axis that maps to LUT, this does not happen.

best
Shalin

mobile: +65-90694182
blog: shalin.wordpress.com<http://shalin.wordpress.com>

Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/people.asp#shalinm


On Tue, Jan 26, 2010 at 6:33 AM, Hoover, Karl <[hidden email]<mailto:[hidden email]>> wrote:
Hello David,

Could you describe the precise conditions under which you see this image 'reversal.' Of course, our intention is that black is 0 and and white is all bits on. Please tell us image size, mode, # bits etc.

Best Regards,
Karl Hoover

________________________________________
From: Knecht, David [[hidden email]<mailto:[hidden email]>]
Sent: Monday, January 25, 2010 14:25
To: Micro-Manager General
Subject: [micro-manager-general] Black screen/white screen

One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave


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Re: [micro-manager-general] Black screen/white screen

Knecht, David
I don't think there should be any circumstance in which saturated pixels are displayed as white.  I can't tell you how many times I have been fooled, and every one of my students runs into this every semester.  I strongly vote to change it if it is possible.  It is a no brainer to me.  Dave

On Jan 26, 2010, at 1:07 PM, Hoover, Karl wrote:

> Shalin,
> Exactly correct this display happens only if auto-stretching is on. So, in your opinion as a knowledgeable user, is the behavior correct, or perhaps the histogram should be 'stretched ' in the other direction?
>
> Best Regards,
> Karl Hoover
> ________________________________________
> From: Shalin Mehta [[hidden email]]
> Sent: Monday, January 25, 2010 17:56
> To: Micro-Manager General
> Subject: Re: [micro-manager-general] Black screen/white screen
>
> Hi Karl and David,
>
> I have noticed this also. However it is a 'feature' and not a 'bug'. It happens when we select 'Auto-stretch' for the look up table. When the whole image is saturated, all pixels are 255 - the entire LUT is stretched (or rather squeezed) to 255. When Auto-stretch is not used, and the user selects the histogram axis that maps to LUT, this does not happen.
>
> best
> Shalin
>
> mobile: +65-90694182
> blog: shalin.wordpress.com<http://shalin.wordpress.com>
>
> Bioimaging Lab, Block-E3A, #7-10
> Div of Bioengineering, NUS Singapore 117574
> website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/people.asp#shalinm
>
>
> On Tue, Jan 26, 2010 at 6:33 AM, Hoover, Karl <[hidden email]<mailto:[hidden email]>> wrote:
> Hello David,
>
> Could you describe the precise conditions under which you see this image 'reversal.' Of course, our intention is that black is 0 and and white is all bits on. Please tell us image size, mode, # bits etc.
>
> Best Regards,
> Karl Hoover
>
> ________________________________________
> From: Knecht, David [[hidden email]<mailto:[hidden email]>]
> Sent: Monday, January 25, 2010 14:25
> To: Micro-Manager General
> Subject: [micro-manager-general] Black screen/white screen
>
> One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave
>
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
> ------------------------------------------------------------------------------
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> [hidden email]<mailto:[hidden email]>
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> ------------------------------------------------------------------------------
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Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)



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Re: [micro-manager-general] Black screen/white screen

Shalin Mehta
Hi Karl,

I think what David says is correct - whenever we have saturated pixels, they should be assigned the highest value in LUT.  Perhaps the solution is to prevent the LUT to be squeezed to one gray level. Then, the saturated pixel will automatically get higher end of the LUT.

best regards,
Shalin
On Wed, Jan 27, 2010 at 6:44 AM, David Knecht <[hidden email]> wrote:
I don't think there should be any circumstance in which saturated pixels are displayed as white.  I can't tell you how many times I have been fooled, and every one of my students runs into this every semester.  I strongly vote to change it if it is possible.  It is a no brainer to me.  Dave

On Jan 26, 2010, at 1:07 PM, Hoover, Karl wrote:

> Shalin,
> Exactly correct this display happens only if auto-stretching is on. So, in your opinion as a knowledgeable user, is the behavior correct, or perhaps the histogram should be 'stretched ' in the other direction?
>
> Best Regards,
> Karl Hoover
> ________________________________________
> From: Shalin Mehta [[hidden email]]
> Sent: Monday, January 25, 2010 17:56
> To: Micro-Manager General
> Subject: Re: [micro-manager-general] Black screen/white screen
>
> Hi Karl and David,
>
> I have noticed this also. However it is a 'feature' and not a 'bug'. It happens when we select 'Auto-stretch' for the look up table. When the whole image is saturated, all pixels are 255 - the entire LUT is stretched (or rather squeezed) to 255. When Auto-stretch is not used, and the user selects the histogram axis that maps to LUT, this does not happen.
>
> best
> Shalin
>
> mobile: +65-90694182
> blog: shalin.wordpress.com<http://shalin.wordpress.com>
>
> Bioimaging Lab, Block-E3A, #7-10
> Div of Bioengineering, NUS Singapore 117574
> website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/people.asp#shalinm
>
>
> On Tue, Jan 26, 2010 at 6:33 AM, Hoover, Karl <[hidden email]<mailto:[hidden email]>> wrote:
> Hello David,
>
> Could you describe the precise conditions under which you see this image 'reversal.' Of course, our intention is that black is 0 and and white is all bits on. Please tell us image size, mode, # bits etc.
>
> Best Regards,
> Karl Hoover
>
> ________________________________________
> From: Knecht, David [[hidden email]<mailto:[hidden email]>]
> Sent: Monday, January 25, 2010 14:25
> To: Micro-Manager General
> Subject: [micro-manager-general] Black screen/white screen
>
> One of the things that I find most challenging in teaching with Micro-manager is that when the image is saturated, it shows as a black screen with values of 255.  This is really confusing to the novice when we train them to recognize black as 0 and 255 as white.  Why is this happening and is there anything I can do to prevent it?  Dave
>
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
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Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)



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Re: [micro-manager-general] Black screen/white screen

Nico Stuurman-4
> I think what David says is correct - whenever we have saturated  
> pixels, they should be assigned the highest value in LUT.  Perhaps  
> the solution is to prevent the LUT to be squeezed to one gray level.  
> Then, the saturated pixel will automatically get higher end of the  
> LUT.

Added this behavior to the code.  You can find it in tomorrow's  
nightly build and the upcoming next release.

Best,

Nico


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