Exploration of Deep Learning Network
Architectures for Volumetric Semantic
Segmentation
Akmalul Khairi Nazaruddin
Electrical and Electronic Engineering Department
Universiti Teknologi PETRONAS
Bandar Seri Iskandar, Malaysia
Abstract—As an active area of research, segmentation of
volumetric data, the form in which most medical data is
represented, faced challenges in the lack of sufficient amount of
data for training. The purpose of this project is to implement and
characterize architectures of deep learning neural network for
three-dimensional image segmentation. Artificial data was used
to circumvent the scarcity of training examples in characterizing
the neural networks for volumetric semantic segmentation.
Additionally, gaussian noise with varying SNR were introduced
to the images to determine to what extent does noise affect the
performance of deep learning networks. Three architectures
were successfully implemented, Fully Convolutional[1], Residual
Blocks[2], and Inception Block[3]. The performance neural
networks were measured by computing the accuracy and
visualizing the results of segmentation. Among the three
implemented architectures, Inception were found to be the most
robust in performance compared to other implementation, that it
could overcome, at certain conditions, class imbalance issue that
was found during the preliminary work of the project. Moreover,
the inception network was also found to have a relatively good
performance with noisy images. Although it is expected that the
performance of the network will not generalize well with real
data, the project provided some insight as to the performance of
deep learning neural networks for volumetric semantic
segmentation.
Keywords—Deep Learning; Semantic Segmentation;
I. INTRODUCTION
Machine Learning is one of the technology with the
potential to revolutionize the way information is utilized in
various fields. At its core Machine Learning algorithms are a
data-driven decision model requiring minimal human
intervention. With the advent of the Age of Big Data and
innovations in hardware technology, a subset of machine
learning, called Deep Learning, has risen to a significant
popularity due its accuracy, efficiency, efficacy and reliability.
Deep learning is an advanced and powerful class of neural
network algorithms that are able to learn complex mapping
between input and output. The learning process occurs during a
phase called training phase in the development lifecycle of a
Deep Learning neural networks. These mappings are learnt
directly from the data being used to train the neural network,
Dr. Eric Ho Tatt Wei
Electrical and Electronic Engineering Department
Universiti Teknologi PETRONAS
Bandar Seri Iskandar, Malaysia
contrasting classical Machine Learning algorithms which
require manual feature extraction feature engineering.
As of today, Deep Learning underlies many advanced
pattern recognition features such as naming object in pictures,
segmentation, and natural language processing. Although
originating from the field of applied artificial intelligence
research, Deep Learning has found many application in various
fields including but not limited to, computer vision[4], control
engineering[5], medicine [6], Internet-Of-Things and the
automotive industry[7].
Deep Learning Neural Network has been shown to be
able to address the more complex tasks in image processing,
such as semantic segmentation. The challenge with training a
deep learning neural network end-to-end is the scarcity of
labeled data. Although there has been researches proposing to
address some issues of a volumetric segmentation[8]–[12],
there is yet an approach that can provide quantitative
measurements for the results of the segmentation. Additionally,
there is no clear relationship between the performance of the
neural network with the choices of architecture, effect of noise
and resource constraints. As such application of deep learning
neural networks for volumetric semantic segmentation is still
an active area of research. Therefore, there is a need to
implement and explore architectural choices of a deep learning
neural networks that can perform efficient semantic
segmentation on volumetric data.
II. BACKGROUND
The project focuses on implementing and characterizing
three deep learning convolutional neural network architectures
for volumetric segmentation.
A. Convolutional Neural Network
Convolutional neural network[13] is a class of artificial
neural network, which was inspired by the vision process
happening in visual cortex. CNN has been the choice
architecture for many deep learning applications which
involve computer vision tasks, such as classification and
segmentation. The basic structure of a convolutional neural
network is a successive convolution of the input layers, which
extracts optimal features from each convolutional layer, with
filters producing feature maps. After the convolution the
features map is passed through an activation function, usually
a ReLu, to introduce non-linearity[14]. Afterwards, these
activated feature maps are either down sampled, which
increases abstraction, through max pooling or go through
another convolution. After several convolutions and max
pooling, the extracted features followed by fully-connected
layers, where high-level reasoning occurs, and outputs of the
previous layer are connected to every input of the next layer.
Output of the fully-connected layer are then connected to a
softmax layer producing probability distribution over N-
number of classes. Fig. 1 shows an example of convolutional
neural network architecture.
Fig. 1. Convolutional Neural Network, AlexNet[8]
B. Training of a Deep Learning Network
Classification task such as semantic segmentation falls
under the supervised learning technique of Deep Learning
neural network. Supervised here is understood as the network
trained by being provided labeled training data. In supervised
learning, the network is given an example pair which consists
of an input (tensors, images) and a desired output value (label
or ground truth image). The learning algorithm is fed with
batches of these examples for analysis and infer mapping
derived from the data to suit the task at hand. The forward
propagation of the training data to the networks initializes
weights in the network try to find the function, while the
backward propagation working with a loss function and an
optimizer (i.e. Stochastic Gradient Descent or Adam[15]
optimizer) work to minimize the loss with each prediction
made after the forward propagations. There are several loss
functions that can be used to guide the learning of the neural
network, most commonly used for image classification is the
cross-entropy loss. Cross-Entropy, to put simply, measures the
distance between two probability distributions. Thus, the
probability distribution with the correct class will have as
shorter distance compared to incorrectly predicted classes. An
optimal scenario for the algorithm is when the algorithms can
classify previously unseen objects or images into the correct
classes.
C. Volumetric Semantic Segmentation
Recently, there has been several approaches[12], [16]–
[18] to automatic image segmentation, while preserving the
information in the depth dimension of volumetric images. As
previously mentioned in the introduction, to directly predict
the segmentation of 3D image is computationally
expensive[8]. [17] proposed a patch-based[19] approach of
convolutional neural network for an automatic 3D
segmentation of brain MRI images where segmentation is
done by taking patches of an image, which predicts the center
voxel, along with its close neighbors. DeepNat[17] used two
networks, hierarchically arranged, one to separate the
background and the foreground and the other was used in the
foreground to anatomically classify 25 brain structures by
implementing multi-task learning. The hierarchical
arrangement of the network was used to counter the class
imbalance problem in patch-based segmentation method.
Additionally, the approach tried to reconcile the issue of the
depth dimension by augmenting the model with spectral
coordinates.
Results of the different methods used during evaluation
are compared based on performance when tested using the
dataset of the MICCAI Multi-Atlas Labeling challenge
P0F1P[20]. [17] used mean Dice volume overlap score, called
Sørensen–Dice coefficient index to measure the accuracy of
the neural network. Increased performance of segmentation
was observed when the network implemented an efficient
fully connected Conditional Random Fields (CRF).
D. Fully Convolutional Neural Network
In the context of semantic segmentation, [16] mentions the
drawbacks in a patch-based approach to segmentation as
in[19], the drawback includes the how the network is
relatively slow and overlaps resulting in redundancy. A novel
approach introduced by [1] called Fully convolutional neural
network is a recent CNN network architecture proposed to
perform semantic segmentation on 2D images. One of the key
advantage of the proposed architecture is that it is able to
receive image with arbitrary input size without requiring pre-
or post-processing. The architecture is constructed by adapting
classifier networks to perform semantic segmentation. This is
achieved as remarked by [1] in that it is possible to view fully
connected layers as convolution with kernel windows
covering the inputs region. By doing the transformation the
network is cast into a fully convolutional neural network.
Building upon the works of [1], [16] proposed the “U-
Net”, a fully convolutional architecture, to reconcile the trade-
off between localization accuracy and context, and also
extending the architecture to require less training data with on
the fly data augmentation, while increasing the precision of
the segmentation. The U-Net architecture have two paths, a
contracting and expansive. A classical CNN architecture of
successive convolutions with ReLu activations was employed
in the contracting path, down sampled with a 2x2 max-pooling
after two convolutions by 3x3 kernels. Mirroring the max-
pooling operations in the contracting path, 2x2 up-convolution
or a more correct term, transposed convolution, which
increases the resolution with reduced number of feature maps.
The output of the transposed convolution is concatenated with
1
https://masi.vuse.vanderbilt.edu/workshop2012
cropped features at the corresponding level of the contracting computational resource, this architectural consideration is
path. motivated by the works of [21].
Similar to FCNN architecture discussed earlier, the key
idea of the architecture is that U-Net architecture uses a 1x1 III. METHODOLOGY
convolutional layer at the output layer, in lieu of classical fully The project methodology will follow the general workflow
connected layers. This technique allows for an added of implementing a deep learning neural network, which are
advantage to the network by being able to segment images of architecture definition, training and evaluation of the network
arbitrary sizes[16]. PhC-U373 and DIC-HeLa datasets were performance.
used to evaluate the performance of the U-Net CNN, these
datasets are part of segmentation task the ISBI cell tracking A. Network Architecture
challenge in 2014 and 2015P1F2,2F3P. One of the first changes to accommodate 3D data was to
change the input layer of the network. Another important
The U-Net architecture however, can only be used to
consideration for segmentation is that in conventional classifier
segment 2D images or low depth 3D images. An extension is
network, the image or data is down sampled for increase
necessary to apply the architecture for 3D image abstractions, thus the size of the image or data is reduced or
segmentation. Research work by [12] proposed an architecture less than that of the input. Segmentation task is a pixelwise, or
which extended the U-Net architecture to using three voxel-wise in 3D, classification which must output a mapping
dimensional convolution. This fully convolutional neural of the pixels or voxels of the input data to output with
network is called the V-Net, although bearing similar features predetermined classes, called segmentation map.
to its 2D counterpart, the U-Net, V-Net not only extended the
U-Net architecture to process 3D images but also introduced a Table 1 shows the base architecture that was used in
novel loss layer to better detect desired features in small project. Notice that in lieu of max pooling layers, a convolution
of size 2 and stride of 2 is used to down sample the 3D image,
regions. Evaluation metrics such as Jaccard Index (IoU) or
this is to allow the network to have further learning in the down
Sørensen–Dice coefficient are common metrics for evaluating
sampling layer, instead of the max pooling layers which are not
the performance of a segmentation, both however are non- trainable parameters. This technique is found in the works of
differentiable, thus not usually optimized directly. A standard [21]which shows improvement in the accuracy of the network.
method to resolve this is to use a proxy loss function such as This architecture will serve as the base architecture that will be
multinomial logistic function or cross-entropy loss for modified to see the effect of changing the channel width and
semantic segmentation. Using a proxy loss function can lead depth of the network.
to decent performances provided that the network parameters
has been setup correctly, using differing functions to guide the
TABLE I. BASE ARCHITECTURE FOR VOLUMETRIC SEMANTIC
algorithm during training and evaluation can lead to poor SEGMENTATION
results in segmentation, especially where there is heavy class
Layers Description Output Dimensionality
imbalance in the training examples. [12] alleviate the problem
1. Input Dimension: 128 x 128 x 128 x 1 128 x 128 x 128 x 1
by providing a loss layer, along with a gradient proof, based 2. Convolution 7 x 7 x 7 4 filters, Activation=ReLU 128 x 128 x 128 x 4
directly on Sørensen–Dice coefficient. [12] concluded that the 3. Convolution 2 x 2 x 2 4 filters, Stride: 2 64 x 64 x 64 x 4
dice-base loss introduced in the paper provide significant 4. Convolution 5 x 5 x 5 4 filters, Activation=ReLU 64 x 64 x 64 x 4
boost in performance of segmentation while also addressing 5. Convolution 2 x 2 x 2 4 filters, Stride: 2 32 x 32 x 32 x 4
the class imbalance problem by not requiring sample re- 6. Convolution 5 x 5 x 5 4 filters, Activation=ReLU 32 x 32 x 32 x 4
weighting when compared to multinomial logistic loss. 7. Convolution 2 x 2 x 2 4 filters, Stride: 2 16 x 16 x 16 x 4
Another important feature of the dice-based loss layer is that 8. Convolution 5 x 5 x 5 4 filters, Activation=ReLU 16 x 16 x 16 x 4

loss can only be used for binary classification, foreground or 9. Convolution 2 x 2 x 2 4 filters, Stride: 2 8x8x8x4

background. 10. Deconvolution Size: 4 x 4 x 4, Stride: 4 32 x 32 x 32 x 4

Furthermore, the V-Net incorporated the use of residual
blocks, introduced by[2], the winner for ILSVRC2015, to
address the vanishing gradients in Convolutional Neural
Network with significant depth. Another architectural
difference between V-Net with its inspirations is that instead
of max-pooling operations to down sample the images, a
convolutional operation with a stride of 2 and a valid padding,
which in essence perform a down sampling with no noticeable
effect on the performance of the network while also reducing
2
http://www.codesolorzano.com/Challenges/CTC/Welcome.ht
ml
3
http://brainiac2.mit.edu/isbi_challenge/
11. Deconvolution Size: 4 x 4 x 4, Stride: 4 128 x128 x 128 x 4
12. Convolution 1 x 1 x 1 4 filters, 1 x 1 x1 Convolution 128 x 128 x 128 x 4
13. Softmax Layer Decision Layer 128 x 128 x 128 x 4
Three implemented neural network architectures were the
classical fully convolutional[1], fully convolutional with
residual blocks[2] and inception blocks[3]. Empirical
evidences show that deep neural network almost always
outperform shallow ones. Residual block[2] were motivated
by the issue in very deep network called vanishing gradients.
Vanishing gradients is the occurrence whereby the gradient
updates of the neuron in earlier hidden layers becomes very
small which essentially means that earlier layer does not learn.
Another problem with arbitrarily adding depth to a neural
network leads to, counter-intuitively, the issue where the
performance of the network actually degrades during training
and evaluation error actually increases. Fig. 2 shows the
architectures that were implemented in the project.
Fig. 2. Implemented CNN Architecture
There are total of seven architectures, 5 classical fully
convolutional, one architecture implementing residual blocks
and one implementing inception blocks. The input convolution
of the first three architecture were varied to investigate the
effect of increasing the width of the network at initial layers,
while the two last two of the classical fully convolutional
implementation sees additional up-convolutional layers to
investigate the effect of more intermediate up-sampling before
performing voxel-wise classification. Residual implementation
incorporates the residual blocks by adding skip connections
between the input convolutional of the block with the output
convolutional before the strided-convolution used for down
sampling the volumes.
B. Training
To circumvent the difficulty of training a deep learning
neural network for volumetric segmentation, the project will
utilize artificial data to train and characterize the performance
of networks. This is motivated by the fact that artificial data
can be generated, in theory, infinitely many, provide access to
perfect ground truth, and easily added noise for observing the
effect of noise with respect to the performance of the deep
learning neural network. Using generated data for training has
some implication on the term epoch in training a deep learning
network. In the context of machine learning, one epoch is
defined as the entirety of examples in the dataset, which means
when an epoch is complete the network has seen every
example in the dataset. This definition of epoch is invalid when
the data being used can be generate infinitely, which implies
that the network will never be able to see or process the
entirety of the training examples. The project will limit the
amount of training examples into 10.000 examples for all
architecture and compare the performance of each. The training
accuracy were logged every 10 steps and evaluation accuracy
at every 2000 steps through the network. The validation was
done on 1000 examples, the average accuracy of these
examples is taken to be the accuracy of the network at
validation. Batch size of 1 were used so that the updating of the
network weight happens at every step through the network and
also to reduce overhead due to processing 3D images. For the
loss function, cross-entropy loss was used as proxy objective
function to guide the segmentation while the gradient optimizer
was ADAM[15] optimizer due to its effectiveness and required
time for convergence.
1) Artifical Data
The data will be generated in the form of 5-dimensional
tensor with each dimension corresponding to batch size,
height, width, depth, and channel number of the data sample
respectively. The synthetic data will be populated with values,
forming a sphere inside the bounding of the specified height,
width and depth. This same data will be used as the sparsely
annotated label. Another advantage of using a synthetic
training data is the theoretically limitless types of shapes and
transformation that can be generated, which can potentially
allow the network to be trained to achieve perfect accuracy.
Fig. 3, shows a data sample with three instances of spheres;
Each sphere has a radius of 20 units in the cartesian
coordinate, whose origin points are generated in a random
fashion.
Fig. 3. Sample Data
Using artificial data for training allows for an informative
insight as to the effect of chosen architecture on the
performance of the neural network with less emphasis
overfitting. Additionally, using artificial data allows for a
study of how the performance of the neural network is
affected by varying degree of noise in the images. The noise to
be added to the images were chosen to be the Gaussian Noise.
Although there are more accurate representaion of noise in
digital images, such as Rician noise in medical images,
gaussian noise was chosen due to its ubiquity in digital images
and relatively simple to implement. The three SNR values that
were genereated for the treaining of the neural netwrok were
noiseless images (SNR: ∞), images with 0dB noise and -10dB
noise. The formula to calculate the amount of noise is be
added is shown in equation 1 and equation 2 from digital
signal processing, where equation 2 is used to calculate the
SNR in dB taking the ratio as pixel intensity in digital images.
(1)
(2)
C. Evaluation
In order to provide a clear result or whether or not there
are improvements or advantage of a neural network over
another neural network, the evaluation metrics must be chosen
carefully. [22] mentioned the importance of using common or
standard evaluation metrics to provide correct inferences of
the results when comparing performances with other methods.
Additionally, [22] asserted that the value of chosen metrics
might varies depending on tasks, or the context for which the will not overfit. Additionally, overfitting were avoided due to
neural network is made. the data being generated on the fly in a random fashion.
For semantic segmentation task, there are several standard
metrics to choose from, the most common is accuracy, the
accuracy used to describe the performance of a segmentation
is quite different than the accuracy used for normal
classification. The difference lies in that the prediction of each
pixels or voxels falls into four cardinalities, TP, FP, TN, and
FN, which are True Positives, False Positive, True Negative
and False Negative[23]. [1] calculated the accuracy of the
network prediction by dividing the intersection between the
prediction made by the network and ground truth of the data
sample with the number of voxels from each classes in Fig. 4. Overall Training and Validation Accuracy (Noiseless)
equation 3[1].
(3)

Where i represent the number of classes and nii represent

the classes which belongs to class i correctly predicted to class
i, and ti represent the total voxels of class i. This evaluation
metric is also called Jaccard Coefficient Index. Class
imbalance is a common issue with neural network for
semantic segmentation, this is especially true with volumetric
data. In order to observe how severe an effect does the class
imbalance has on the performance of the neural network, the
pixel accuracy will be computed for a whole image case and Fig. 5. Overall Training and Validation Accuracy (0db Noise)
per class case. This is achieved by extracting class masks from
the ground truth of the sample and computing Intersection-
over-Union for each.
In addition to numerical evaluation, visualizing the results
of the segmentation will provide a clearer overview of the
networks performance. This is achieved by plotting the
predicted voxel color scheme to differentiate between the
predicted classes. Furthermore, visualization will also help in
checking whether there are any issues with the numerical
calculation itself.
Fig. 6. Overall Training and Validation Accuracy (-10db Noise)
IV. RESULTS AND DISCUSSION
In characterizing the performance of deep learning This is an interesting finding that comparison between
networks, accuracy during training do no represent the actual training and evaluation with 10.000 training examples show
performance of the neural network. However, it is a useful negligible bias. The evaluation accuracy was calculated by
heuristic tool to observer whether the neural netwrok can taking the sample mean of 1000 images generated every 2000
learns to perform the task. Moreover, training accuracy is used training steps through to network.
to determine if the neural netwrok exhibit overfitting. This
section will discuss the finding from characterization of the B. Class Imbalance
deep learning neural netwrok for volumetric semantic
segmentation. With overfitting circumvented by using the artificial
data, another issue was found during characterization of the
neural network. Class imbalance is a common issue in
A. Overfitting
semantic segmentation where there are more examples of one
Overfitting of the network can be observed by comparing class of compared to other thus skewing the network to be
the training accuracy with validation accuracy. This is shown more tuned to detect the class with more abundant examples,
Fig. 4, 5 and 6. Where training accuracy is in the first subgraph such as the background. This can be observed from the results
while the validation accuracy is in the second subgraph.
of network accuracy where even for the classical fully
Overfitting happens where there is a significant bias between
convolution with relatively small network capacity (A1), the
the training and evaluation accuracy. The results show that
overfitting is not observed for all seven architectures across accuracy reaches over 95 %. The effect of class imbalance can
three different SNR values. This is consistent with the be inferred by overseeing comparing the class-wise accuracy
assumption that with enough training example the networks of each network. Fig. 7 show the accuracy of each class in of
the neural network trained with noiseless images.

Fig. 7. Class-wise Validation Accuracy (Noiseless)
Fig. 8. Class-wise Validation Accuracy (0dB Noise)
Fig. 9. Class-wise Validation Accuracy (-10dB Noise)
The results imply two important points, the first is that the
heavy class imbalance in the training examples prevents the
network from learning to segment classes other than the
background class (Class 0) which is guided by proxy loss
function, cross-entropy loss for multi-class classification. The
loss function used to guide the learning of the neural network
does not provide sufficient performance for the architectures
which implement the classical convolutional neural network,
the varying width at the input and adding more up-sampling
layers shows negligible effect on the accuracy of other classes.
Another is that deeper network, specifically implementation of
inception and residual block, seems to be able to overcome the
class imbalance, as can be seen across three different SNR
values in the images. However, the results by no means
conclusively implies that shallower neural networks are unable
to perform volumetric segmentation, it only shows that to
perform multi-class classification using cross-entropy loss on
shallower network results in neural networks that are more
tuned to classify classes that has more examples in the data,
which in the case of the project is the background class. The
implication is that using a more a suitable loss function to
guide the learning might allow shallower netwrok to perform
volumetric semantic segmentation. Cross-entropy loss was
used due to the non-differentiable nature the accuracy measure
selected to measure the performance of the neural networks.
Optimization lead directly by the accuracy metric with which
we measure the performance of the network should provide
better segmentation results as loss function based on Dice-
Sorensen coefficient proposed by [12], however the proposed
loss were only able to perform binary volumetric semantic
segmentation. Fig. 10, 11 and 12 shows segmentation results
for volumetric segmentation from three different
implementations of fully convolutional neural network, A1,
A6 and A7 respectively, across all three different SNR values.
Fig. 10. Segmentation results on noiseless images
Fig. 11. Segmentation results on images with 0dB Noise
Fig. 12. Segmentation results on images with -10dB Noise
C. SNR Study
The effect of noise on the performance of networks on
volumetric segmentation can be observed in Fig. 7 to 12. The
amount of noise does not seem to adversely affect the
performance of network with inception blocks. Architecture
A6, which was shown to overcome class imbalance issue in
noiseless images seems to be affected quite heavily by the
noise introduced for SNR study, in that it failed to learn to
classify classes which are not the background class, where it
was able to achieve more than 99% accuracy. This might imply
that the addition of noise into the images increase the severity
of class imbalance or that it shifts the mean and variance of the
data sample thereby increasing the difficulty for the network to
find the optimal mapping. Architecture A7 shows a more
interesting result where it is able to achieve a similar
performance on very noise image (-10dB) as with noiseless
images, however fails to perform segmentation for images with
0db noise. The cause of this failure might be due to the
occurrence whereby the optimizer is stuck in a local minimum
and is not able to find a way out, possibly caused by the
addition of noise. For the classical implementations of fully
convolutional neural network it is more difficult to provide a
general interpretation of how the amount of noise in the images
affect their performance due to the class imbalance issue.
V. CONCLUSION
In conclusion, the project has successfully implemented and
characterize three fully convolutional architecture which
includes implementation of state of the art architectural choices
which were shown to allow deep neural netwrok to achieve
significantly better performance. Deeper neural networks are
quite robust to, in certain conditions, to overcome the issue of
class imbalance while also performing remarkably well on
images with signal-to-noise ratio less than one. However, the
performance shown in this paper is limited to applications of
deep learning neural network trained and evaluated using
artificial data with access to abundance of examples with
perfect ground truth. Although, similar performance cannot be
expected when dealing with real data with high variability, this
project provides an informative exercise in characterization of
deep learning neural network for volumetric semantic
segmentation.
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