AngioUnet
A Convolutional Neural Network for Vessel Segmentation in Cerebral DSA Series
Christian Neumann
1
, Klaus-Dietz T
¨
onnies
2
and Regina Pohle-Fr
¨
ohlich
1
1
Institute for Pattern Recognition, Hochschule Niederrhein University of Applied Sciences, Krefeld, Germany
2
Department of Simulation and Graphics, Otto-von-Guericke University of Magdeburg, Germany
Keywords:
CNN, Cerebral, DSA Series, Vessel Segmentation.
Abstract:
The U-net is a promising architecture for medical segmentation problems. In this paper, we show how this
architecture can be effectively applied to cerebral DSA series. The usage of multiple images as input allows
for better distinguishing between vessel and background. Furthermore, the U-net can be trained with a small
corpus when combined with useful data augmentations like mirroring, rotation, and additionally biasing. Our
variant of the network achieves a DSC of 87.98% on the segmentation task. We compare this to different
configurations and discuss the effect on various artifacts like bones, glue, and screws.
1 INTRODUCTION
In the past, segmentation tasks have been solved with
a wide variety of methods and combinations of those.
In the medical image processing context, one specific
task is the segmentation of single organs, homogene-
ous structures like bones or – in our case – vessels.
The difficulty of medical applications lies in the usage
of a lot of modalities. Between a pair of modalities,
the gray values rarely show any correspondence. This
means that we still have to build or adapt methods to
every single new modality in order to solve the given
task successfully.
In the context of vessel segmentation, the gene-
rally used scheme consists of preprocessing, enhance-
ment, thresholding, and possibly postprocessing. The
preprocessing commonly is needed to reduce noise
and transform the data globally e.g. normalization.
The threshold can be for example a single value or
adaptive to a small region. In summary, the segmen-
tation task consists of three major parts. These are
edge detection, noise suppression, and non linear con-
trast enhancement. All these tasks would have multi-
ple parameters, if solved with conventional methods.
By using deep learning, we can train a neural network
that is optimal for a given dataset.
The segmentation is part of the preprocessing in a
medical 2D/3D-registration project. For the treatment
of arteriovenous malformations (AVM) using radio-
surgical devices careful planning of the radiation cen-
troids is necessary in order to protect healthy tissue
and successfully embolize the nidus. In our project,
the available modalities are a digitally subtraction an-
giography (DSA) and a partial MRI of the head. The
DSA series will be some days old and may have diffe-
rent absolute gray values due to different imaging de-
vices and settings. The MRI on the other hand is made
on the same day as the treatment, in fact the gamma
knife treatment can start less than an hour later, while
the planning is done manually. For the registration
task, it is important to segment the vessels that are
visible in both modalities and to keep the spatial reso-
lution of the result as high as possible. In this paper,
we will look at the detection of vessels in the DSA
series. Besides, we plan to adapt the same network
to the MRI images as well i.e. train the same network
end-to-end on two different modalities by using a dif-
ferent dataset and possibly tuning of hyperparameters,
only.
Here we apply the U-net (Ronneberger et al.,
2015) architecture to our segmentation task. We dis-
tinguish two classes – vessels and background. Addi-
tionally, we are mostly interested in the arteries, be-
cause most veins will not be visible in a correspon-
ding MRI. Therefore vein suppression is important,
too. The given modality generally gives a good con-
trast between vessels and the background. The pro-
blem of separating the vessels (dark) from the back-
ground (bright) seems to be easy at first. But the clas-
ses are not separable by a single threshold. The back-
ground is noisy and there is a slight shadow of bones
and more left. In order to classify images from this
Neumann, C., Tönnies, K-D. and Pohle-Fröhlich, R.
AngioUnet - A Convolutional Neural Network for Vessel Segmentation in Cerebral DSA Series.
DOI: 10.5220/0006570603310338
In Proceedings of the 13th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications (VISIGRAPP 2018) - Volume 4: VISAPP, pages
331-338
ISBN: 978-989-758-290-5
Copyright © 2018 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved
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