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

[Andras Lasso]

Have you tried segmentation tools in 3D Slicer? There is a multi-label watershed segmentation tool that works in 3d (http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Editor#WatershedFromMarkers), there are also a number of other generic semi-automatic segmentation tools (such as GrowCut) and a few fully-automatic specialized tools (for brain, airways, etc). Download the nightly build and also checkout the Segmentation category in the Extension Manager.

Andras

From: Dr. Roman Grothausmann<mailto:grothausmann.roman at mh-hannover.de>
Sent: ‎Monday‎, ‎August‎ ‎11‎, ‎2014 ‎1‎:‎15‎ ‎AM
To: itksnap-users at googlegroups.com<mailto:itksnap-users at googlegroups.com>
Cc: ITK Mailing List<mailto:insight-users at itk.org>

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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