[Insight-users] Surface smoothing of labels

[Richard Beare]

You need to think quite carefully about what you want to achieve with
the smoothing. Any linear-ish smoother applied to objects individually
is likely to lead to them overlapping. This may be OK if you are only
after visualization and/or are happy representing each image in a
separate image.

If you want to do something that keeps the properties of a label image
then a morphological opening is a simple choice that won't introduce
overlap. You can pull out label objects perform an opening on each
one, put them back together. There are ways of operating directly on
the label set quite efficiently -
"Parallel Algorithms via Scaled Paraboloid Structuring Functions for
Spatially-Variant and Label-Set Dilations and Erosions", Beare and
Jackway, DICTA 2011. The code is ITK-based, but I haven't got around
to packaging it for release, let me know if it sounds interesting
enough to make the effort.

Your other option is to smooth first - don't be tempted by using a
chamfer (approximate) distance transform - use an exact one and smooth
it. Also, as distance transforms are typically used to split cells, it
suggests that you have some segmentation process prior to this. If
this is the case you may benefit from smoothing the raw image further
prior to segmentation.

On Sat, Jan 19, 2013 at 2:51 PM, Thomas Seidel <seidel at cvrti.utah.edu> wrote:
> Hi,
>
> I have segmented cells in tissue sections using a morphological watershed.
> So the output is a label image.
> The segmentation result is not bad. However, the surfaces of the cells seem
> to have disturbances and some tiny artifacts (probably due to the distance
> map which I used as gradient image).
>
> So I am looking for a method to smooth the surfaces of the cells without
> loosing to much detail. I found the  itkAntiAliasBinaryImageFilter, but it
> requires a binary image as input. I cannot reduce the label image to a
> binary image because sometimes the cells have no background between them,
> which means that I cannot separate them again.
>
> Is there any surface smoothing filter which operates on a label image?
> How can I transform a label image into an input image for a level set
> filter?
>
> Thanks,
> Thomas
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>