missing kernel or block size in equalize_adapthist

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Kai Wiechen

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May 25, 2015, 2:49:53 PM5/25/15
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Hello,

I am using equalize_adapthist after color deconvolution and some morphological operations to enhance local contrast of nuclei in histological images. There are different results when applying equalize_adapthist when using small patches and larger size whole images (left small patch, right large size whole image). The CLAHE implementation in ImageJ has a 'block size' parameter and the implementation in Pixinsight has a 'Kernel size' parameter to get results depending on the local context. Is it possible to 'simulate' this behaviour with scikit-image?

Best regards,

Kai







Steven Silvester

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May 25, 2015, 6:54:34 PM5/25/15
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Hi Kai,

Do the `n_tiles*` arguments not meet your needs?  By defining the number of tiles in X and Y, you are equivalently setting a block size.



Regards,

Steve

Kai Wiechen

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May 26, 2015, 2:58:55 AM5/26/15
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Hi Steve,

but these parameters are limited to the range 1..16. The small test patches are 150x150 pixels, the complete images have 1920x1448 pixels. I have applied equalize_adapthist here with default parameters (n_tiles=8).

Best regards,

Kai

Steven Silvester

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May 26, 2015, 9:17:01 PM5/26/15
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Hi Kai,

Is the issue that you want finer grain control of the block size?  If so, that would require a substantial rewrite.

Please feel free to open an issue on Github if that is the case.


Regards,

Steve


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Kai Wiechen

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May 28, 2015, 2:35:49 PM5/28/15
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Hi Steve,

yes, I would like to have finer control of block/kernel size to obtain similar results if I apply this to small test patches or the larger complete image. Is there any reason to limit ntiles_x/y to 16?

Regards,

Kai

Steven Silvester

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May 28, 2015, 4:25:44 PM5/28/15
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Hi Kai,

The limits were set based on the original implementation, but there is no reason they need to stay at 16.  Using an arbitrary size tile is what would take a substantial rewrite.  Looking at your numbers, it looks like a 13x10 block size will get you ~150x150 tile size.  At the full 16x16, you'd have 120x90 pixels.


Regards,

Steve

Steven Silvester

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Jun 6, 2015, 11:54:30 AM6/6/15
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Hi Kai,

We are having a discussion now about how to fix/improve the adapthist block handling:  https://github.com/scikit-image/scikit-image/issues/1541.


Regards,

Steve

On Monday, May 25, 2015 at 1:49:53 PM UTC-5, Kai Wiechen wrote:
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