Medical image segmentation has played an important
role in medical analysis and widely developed for many clinical
applications. Deep learning-based approaches have achieved
high performance in semantic segmentation but they are limited
to pixel-wise setting and imbalanced classes data problem. In
this paper, we tackle those limitations by developing a new
deep learning-based model which takes into account both higher
feature level i.e. region inside contour, intermediate feature level
i.e. offset curves around the contour and lower feature level i.e.
contour. Our proposed Offset Curves (OsC) loss consists of three
main fitting terms. The first fitting term focuses on pixel-wise level
segmentation whereas the second fitting term acts as attention
model which pays attention to the area around the boundaries
(offset curves). The third terms plays a role as regularization
term which takes the length of boundaries into account. We
evaluate our proposed OsC loss on both 2D network and 3D
network. Two common medical datasets, i.e. retina DRIVE and
brain tumor BRATS 2018 datasets are used to benchmark our
proposed loss performance. The experiments have shown that
our proposed OsC loss function outperforms other mainstream
loss functions such as Cross-Entropy, Dice, Focal on the most
common segmentation networks Unet, FCN.
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A Multi-task Contextual Atrous Residual Network for Brain Tumor Detection & Segmentation
In recent years, deep neural networks have achieved
state-of-the-art performance in a variety of recognition and
segmentation tasks in medical imaging including brain tumor
segmentation. We investigate that segmenting a brain tumor is
facing to the imbalanced data problem where the number of pixels
belonging to the background class (non tumor pixel) is much
larger than the number of pixels belonging to the foreground
class (tumor pixel). To address this problem, we propose a multitask
network which is formed as a cascaded structure. Our model
consists of two targets, i.e., (i) effectively differentiate the brain
tumor regions and (ii) estimate the brain tumor mask. The first
objective is performed by our proposed contextual brain tumor
detection network, which plays a role of an attention gate and
focuses on the region around brain tumor only while ignoring the
far neighbor background which is less correlated to the tumor.
Different from other existing object detection networks which
process every pixel, our contextual brain tumor detection network
only processes contextual regions around ground-truth instances
and this strategy aims at producing meaningful regions proposals.
The second objective is built upon a 3D atrous residual network
and under an encode-decode network in order to effectively segment
both large and small objects (brain tumor). Our 3D atrous
residual network is designed with a skip connection to enables the
gradient from the deep layers to be directly propagated to shallow
layers, thus, features of different depths are preserved and used
for refining each other. In order to incorporate larger contextual
information from volume MRI data, our network utilizes the
3D atrous convolution with various kernel sizes, which enlarges
the receptive field of filters. Our proposed network has been
evaluated on various datasets including BRATS2015, BRATS2017
and BRATS2018 datasets with both validation set and testing
set. Our performance has been benchmarked by both regionbased
metrics and surface-based metrics. We also have conducted
comparisons against state-of-the-art approaches
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- Award ID(s):
- 1946391
- NSF-PAR ID:
- 10321627
- Date Published:
- Journal Name:
- 2020 25th International Conference on Pattern Recognition (ICPR)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Medical image segmentation is one of the most challenging tasks in medical image analysis and widely developed for many clinical applications. While deep learning-based approaches have achieved impressive performance in semantic segmentation, they are limited to pixel-wise settings with imbalanced-class data problems and weak boundary object segmentation in medical images. In this paper, we tackle those limitations by developing a new two-branch deep network architecture which takes both higher level features and lower level features into account. The first branch extracts higher level feature as region information by a common encoder-decoder network structure such as Unet and FCN, whereas the second branch focuses on lower level features as support information around the boundary and processes in parallel to the first branch. Our key contribution is the second branch named Narrow Band Active Contour (NB-AC) attention model which treats the object contour as a hyperplane and all data inside a narrow band as support information that influences the position and orientation of the hyperplane. Our proposed NB-AC attention model incorporates the contour length with the region energy involving a fixed-width band around the curve or surface. The proposed network loss contains two fitting terms: (i) a high level feature (i.e., region) fitting term from the first branch; (ii) a lower level feature (i.e., contour) fitting term from the second branch including the (ii1) length of the object contour and (ii2) regional energy functional formed by the homogeneity criterion of both the inner band and outer band neighboring the evolving curve or surface. The proposed NB-AC loss can be incorporated into both 2D and 3D deep network architectures. The proposed network has been evaluated on different challenging medical image datasets, including DRIVE, iSeg17, MRBrainS18 and Brats18. The experimental results have shown that the proposed NB-AC loss outperforms other mainstream loss functions: Cross Entropy, Dice, Focal on two common segmentation frameworks Unet and FCN. Our 3D network which is built upon the proposed NB-AC loss and 3DUnet framework achieved state-of-the-art results on multiple volumetric datasets.more » « less
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/icpr48806.2021.9412414
