[ITK-users] patch to add a global hierarchical watershed segmentation mode to itksnap

[Dr. Roman Grothausmann]

Dear mailing list members,


Finally, I got my idea about an interactive hierarchical Watershed 
SegmentationEditor realized. The idea originates from the SegmentationEditor of 
the InsightApplication demonstrated here: 
http://www.insight-journal.org/browse/publication/70

I decided to add such functionality to itksnap as it is the successor of the 
SegmentationEditor. The additions consist of a Click'n'Join mode, which either 
allows to join or split labels of the current segmentation by clicking, or 
instead uses a Global Watershed label image as a label source. The great feature 
of the itkWatershedFilter allows the level of the watershed hierarchy to be 
changed on-the-fly.
The patch is against itksnap-3.0.0 and in beta-testing stage. Loading from files 
and "back" buttons are not yet implemented.
Please feel free to test it too!

Regards,
Roman

On 11/08/14 07:15, Dr. Roman Grothausmann wrote:
> Dear mailing list members,
>
>
> For a long time now I've been searching for a replacement of the old
> SegmentationEditor (part of the InsightApplications) which I could not get to
> work even with older ITK-3.x. Somewhere I was told that it was integrated and
> maintained within itksnap. However the only tool in itksnap based on watershed
> segmentation seems to be the adaptive brush. It is very handy, but
> time-consuming in 3D and only for local segmentations. In contrast the
> SegmentationEditor used a global hierarchical watershed segmentation to pick
> labels from, see e.g. the video linked here:
> http://www.insight-journal.org/browse/publication/70
> Quite often now I've stumbled over data, that would likely have profited a lot
> of such a tool for segmentation.
>
> If such a tool working with ITK-4.x does not exist any more, I thought of
> implementing it as a global WS segmentation mode in itksnap. That way making the
> tool easier to find, to use and to ensure maintenance (should it be integrated
> into the itksnap code base in the end) and also avoiding recoding a GUI with
> mouse interaction and such.
>
> My current idea is to start, similar to the snake-tool, with pre-filtering like
> smoothing and optional edge-detection.
> Then the main edit mode to consist of the usual 4 subwindows showing an overlay
> of the grey-image and the watershed segmentation of the hierarchical WS-filter
> (hWS), side-by-side to another label-dataset (loaded like a tiled overlay) which
> consist of the actually chosen labels from the hWS as the final data (FD).
> The interaction I'm considering would be to LMB click on a label in the hWS
> which is then added to the FD as the current fg label, or removed with a RMB.
> The hierachrchy level of the hWS could be controlled by a slider or the mouse
> wheel + Shift in nearly real time if some region demands higher or lower
> detailed segmentation. When the fg label is changed, the segmentation added or
> removed with further mouse interactions would modify the new fg label.
> When all is done and the global WS mode is left, the FD label-dataset is added
> to the main segmentation of itksnap.
>
> Would that be possible to implement in itksnap 3.x?
> What source files of the itksnap code base should I look at for:
> - the pre-filtering mode of the snake (for the smoothing and edge detection)
> - the mouse interactions (for e.g. adding the whell + Shift interaction)
> - possible examples for the dual layout
>
> Thanks for any comments, help or hints.
> Roman
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574
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