Re: Chromatin condensation

[Lendl,Thomas]

Hi all,

We recently had a user request for measuring chromatin condensation and I wonder if anyone of you did something similar already. We tried to use a normalized StdDev. but it didn't give any proper result.  Trying to shape out the Structures via LoG also didn't lead anywhere. Is there any technique or statistical parameter for describing these different textures?

https://www.dropbox.com/sh/1z36xtv0fmwc21x/AACpTWFQ2Yb2G9zpBtG-seoZa?dl=0

Thanks in advance,
Thomas

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[Olivier Burri]

Hi Thomas,

I had some success in calibrating the chromatin condensation using the Texture Analyzer http://rsb.info.nih.gov/ij/plugins/texture.html

On your images:
Cropped the Z stacks to contain slices with nuclei
Ran the GLCM Texture plugin with a step size of 3 pixels

Looked at the Average Contrast output of each image and got these values

Control 229.209
Mid 205.782
Condensed 135.794

What I would suggest is try different step sizes to find the one that maximizes the delta between the conditions and perhaps use that.

You can also try the other metrics from the plugin, which have a similar trend (Except for Correlation, which makes sense);

Best

Oli

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[Lendl,Thomas]

Hi Oli,

Thanks a lot for your help, this looks promising. I'm just not sure how to interpret the result because It's somehow counterintuitive to have a lower contrast in more structured objects. Anyway I'll do a testrun on a couple more images to see if the output is consistent.

Best,
Thomas

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Burri Olivier
Sent: Montag, 03. August 2015 14:50
To: [hidden email]
Subject: Re: Chromatin condensation

Hi Thomas,

I had some success in calibrating the chromatin condensation using the Texture Analyzer http://rsb.info.nih.gov/ij/plugins/texture.html

On your images:
Cropped the Z stacks to contain slices with nuclei Ran the GLCM Texture plugin with a step size of 3 pixels

Looked at the Average Contrast output of each image and got these values

Control 229.209
Mid 205.782
Condensed 135.794

What I would suggest is try different step sizes to find the one that maximizes the delta between the conditions and perhaps use that.

You can also try the other metrics from the plugin, which have a similar trend (Except for Correlation, which makes sense);

Best

Oli

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[Olivier Burri]

Hi Thomas

This is the contrast of the co-occurrence matrix, not the contrast of the image. Increasing the step size might reverse the trend.


 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Lendl,Thomas
> Sent: Monday, August 3, 2015 15:44
> To: [hidden email]
> Subject: Re: Chromatin condensation
>
> Hi Oli,
>
> Thanks a lot for your help, this looks promising. I'm just not sure how to
> interpret the result because It's somehow counterintuitive to have a lower
> contrast in more structured objects. Anyway I'll do a testrun on a couple
> more images to see if the output is consistent.
>
> Best,
> Thomas
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Burri Olivier
> Sent: Montag, 03. August 2015 14:50
> To: [hidden email]
> Subject: Re: Chromatin condensation
>
> Hi Thomas,
>
> I had some success in calibrating the chromatin condensation using the
> Texture Analyzer http://rsb.info.nih.gov/ij/plugins/texture.html
>
> On your images:
> Cropped the Z stacks to contain slices with nuclei Ran the GLCM Texture
> plugin with a step size of 3 pixels
>
> Looked at the Average Contrast output of each image and got these values
>
> Control 229.209
> Mid 205.782
> Condensed 135.794
>
> What I would suggest is try different step sizes to find the one that
> maximizes the delta between the conditions and perhaps use that.
>
> You can also try the other metrics from the plugin, which have a similar trend
> (Except for Correlation, which makes sense);
>
> Best
>
> Oli
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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