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Paper

#### How to Extract the Geometry and Topology from Very Large 3D Segmentations

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##### Fulltext (public)

arXiv:1009.6215.pdf

(Preprint), 2MB

##### Supplementary Material (public)

There is no public supplementary material available

##### Citation

Andres, B., Koethe, U., Kroeger, T., & Hamprecht, F. A. (2010). How to Extract the Geometry and Topology from Very Large 3D Segmentations. Retrieved from http://arxiv.org/abs/1009.6215.

Cite as: http://hdl.handle.net/11858/00-001M-0000-0018-9A86-F

##### Abstract

Segmentation is often an essential intermediate step in image analysis. A
volume segmentation characterizes the underlying volume image in terms of
geometric information--segments, faces between segments, curves in which
several faces meet--as well as a topology on these objects. Existing algorithms
encode this information in designated data structures, but require that these
data structures fit entirely in Random Access Memory (RAM). Today, 3D images
with several billion voxels are acquired, e.g. in structural neurobiology.
Since these large volumes can no longer be processed with existing methods, we
present a new algorithm which performs geometry and topology extraction with a
runtime linear in the number of voxels and log-linear in the number of faces
and curves. The parallelizable algorithm proceeds in a block-wise fashion and
constructs a consistent representation of the entire volume image on the hard
drive, making the structure of very large volume segmentations accessible to
image analysis. The parallelized C++ source code, free command line tools and
MATLAB mex files are avilable from
http://hci.iwr.uni-heidelberg.de/software.php