EncapNet-3D and U-EncapNet
for Cell Segmentation
Takumi Sato
Department of Electrical and Electronic Engineering
Meijo University
1-501 Shiogamaguchi, Tempaku-ku, Nagoya 468-8502, Japan
193427015@ccalumni.meijo-u.ac.jp
Abstract—EncapNet is a kind of Capsule network that
significantly improved routing problems that has thought to be
the main bottleneck of capsule network. In this paper, we
propose EncapNet-3D that has stronger connection between
master and aide branch, which original EncapNet has only
single co-efficient per capsule. We achieved this by adding 3D
convolution and Dropout layers to connection between them. 3D
convolution makes connection between capsules stronger. We
also propose U-EncapNet, which uses U-net architecture to
achieve high accuracy in semantic segmentation task.
EncapNet-3D has successfully accomplished to reduce network
parameters 321 times smaller compared to U-EncapNet, 52
times smaller than U-net. We show the result on segmentation
problem of cell images. U-EncapNet has advanced performance
of 1.1% in cell mean IoU in comparison with U-net. EncapNet-
3D has achieved 3% increase in comparison with ResNet-6 in
cell membrane IoU.
Keywords—Capsule Network, EncapNet, Cell Segmentation
I. INTRODUCTION
Convolutional neural network (CNN) has achieved high
accuracy in many tasks. But CNN has some problems such as
the lack of location information by connecting many
convolution layers. Capsule Network [1] has been introduced
to solve the problem. Capsule Network has two key features;
capsule and routing-by-agreement. Capsule is a group of
feature represented as a vector instead of scalar. A single
capsule can represent numerous features while CNN can only
represent one feature at a time. Preserving features together in
form of capsule is very efficient way rather than keeping
features in a separate manner. This property can be seen that
many capsule networks succeed to accomplish higher
accuracy with fewer layer than CNN. Routing-by-agreement
is a pooling layer for capsules. Unlike max pooling, which
loses precise location information every time it has been used,
routing-by-agreement will learn to preserve location
information no matter how many times routing has been used.
Dynamic routing was the first routing-by-agreement to be
introduced. It used huge parameters for pooling. Dynamic
routing had achieved high accuracy in dataset like MNIST.
However, because of the huge parameters, it had difficulty
getting high accuracy in datasets which has bigger input image
size than MNIST. Recently, EncapNet [2] has been introduced
which achieved very high accuracy in CIFAR10, CIFAR100,
SVHN and ImageNet. EncapNet shared a new routing-by-
agreement algorithm called approximate routing.
Approximate routing has succeeded to significantly improve
routing-by-agreement, which has thought to be the one of the
biggest bottlenecks of capsule network.
In this paper, we prove that EncapNet can achieve high
accuracy not only in classification but also in semantic
segmentation. SegCaps[4] has succeeded to achieve high
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Kazuhiro Hotta
Department of Electrical and Electronic Engineering
Meijo University
1-501 Shiogamaguchi, Tempaku-ku, Nagoya 468-8502, Japan
kazuhotta@meijo-u.ac.jp
accuracy on binary segmentation tasks but not to multi
segmentation task. We propose U-EncapNet which is based
on EncapNet that has achieved high accuracy on multi-classes
classification such as ImageNet-1k. U-EncapNet uses U-net
architecture which has achieved high performance in semantic
segmentation. We also used dropout for reducing overfitting.
We consider that capsule is very efficient way to express
feature map. Before EncapNet was introduced, routing-by-
agreement had very huge parameters and efficiency was
hidden behind it. Using approximate routing, we can now
reduce network parameters, with very small decrease of
accuracy. Recently, network architecture which can produce
high accuracy has been proposed such as ENET[14],
MobileNet[15] and ShuffleNet[16]. Proving that Capsule
Network can achieve high accuracy in low parameters will
expand the possibilities of Capsule Network which only few
paper [17] has mentioned about it.
We also propose EncapNet-3D, which has stronger
connection between master and aide branch compared to
EncapNet. EncapNet uses group convolution to separate each
capsule. EncapNet does not have enough connection between
capsules since most of them are divided by groups. EncapNet-
3D used 3D convolution on co-efficient between master and
aide branch to increase connection between capsule. This
makes EncapNet-3D perform very close accuracy with only
one block. EncapNet-3D has achieved 52 times smaller
network parameter than U-net and has achieved very close
accuracy in mean IoU compared to U-net.
We used 3-class segmentation dataset, images of liver cell
from mice to show that U-EncapNet outperforms U-net. We
also compared EncapNet-3D with resnet-6 which has only
single resnet block. EncapNet had maximum of 5% increase
in comparison with resnet-6 in mIoU. We also used
segmented anisotropic ssTEM dataset [3] which is 5-class
segmentation dataset.
This paper is organized as follows. In section 2, we
introduce related works in capsule network and real time
semantic segmentation. We are going to introduce our
proposed method EncapNet-3D in section 3 and U-EncapNet
in section 4. We show the experimental results of EncapNet-
3D and U-EncapNet on mice liver image dataset and
anisotropic ssTEM dataset in section 5. Conclusions and
future works are described in section 6.
II. RELATED WORKS
Capsule network [1] was introduced by S.Sabour et al. and
has been adopted to various tasks. SegCaps [4] has
successfully adopted it to object segmentation using U-net
architecture and successfully reduced dynamic routing
 Figure 1 Network architecture of EncapNet-3D
parameter size by using local capsules instead of using all the structures compared to CNN. Capsule Network tends to
capsules in the layer. J.Gong at el. [5] adopted Capsule
network to sequence Encoding. F.Vedperini [6] applied it to
SED task.
Due the huge parameters used in dynamic routing, Capsule
network had difficulty achieving high accuracy in some tasks
that has large input image size. To improve the Capsule
network, improving one of the biggest bottlenecks of capsule
network which was the dynamic routing is one of the main
goals in research. There are many improvements about
dynamic routing. D.Wang et al. [7] has formulated Dynamic
routing as an optimization problem. This idea has been used
in EncapNet which uses OT loss to enforce the network
regularization. G.Hinton et al. [8] proposed Matrix capsules
which uses matrix to reduce parameters and EM routing for
routing-by-agreement which is more superior than dynamic
routing but had huge parameter size like dynamic routing .
K.Duarte at el. [9] proposed capsule-pooling to reduce
parameters in matrix capsule and applied it for action
detection. A.Mobiny et al. [10] proposed 3D capsule Network
and reduced coefficient parameters for dynamic routing.
M.Bahadori proposed Spectral Capsule Networks for
leaning-to-diagnose problem which preforms better than
Matrix Capsules. L.Zhang at el. proposed CapProNet [11]
which learns group of capsule subspaces to represent each
class.MS-CapsNet [12] proposed Dropout for capsule and
achieved higher accuracy in CIFAR10 than original capsule
network. These routing improvements are likely to be
specialized to certain tasks and are difficult to apply to
another tasks. In semantic segmentation, pre-training with
datasets like classification task helps to achieve higher
accuracy in U-net [13]. In order to do this in capsule network, capsule network [8] has used 3D convolution instead of 2D
routing algorithm which can achieve high accuracy in
classification and segmentation is needed.
U-net [13] archived high performance in semantic
segmentation. In cell segmentation, some methods [18-22]
had been proposed. A.Paszke [14] proposed ENet, that has
very high performance considering the small parameters used
in the network. MobileNet [15] uses depthwise separable
convolution to achieve high accuracy in low parameters.
ShuffleNet [16] uses group convolution and channel shuffle
and succeeded to reduce network parameters. A.Lin et al. [17]
showed that capsule network can capture global manifold
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achieve higher accuracy in very simple network compared to
CNN. These networks have very few parameters but do not
have network depths as shallow as capsule network. Our
EncapNet-3D only uses one block which means shallow
network and has very few parameters at the same time.
III. ENCAPNET-3D
EncapNet has achieved very high accuracy on ImageNet-
1K. EncapNet uses approximate routing which greatly
reduces parameters used in routing. Approximate routing
divides input capsule into two branches; the master and aide
branch as.
ܵ௝ ൎ ݉௔௜ௗ௘ ‫ݒ‬ො௠௔௦௧௘௥ ൅ ݉௠௔௦௧௘௥ ‫ݒ‬ො௔௜ௗ௘ (1)
where ܵ௝ is an output of j-th channel and ‫ݒ‬ො is the input
capsule for approximate routing. Master branch ‫ݒ‬ො௠௔௦௧௘௥ uses
group convolution to see only capsules that are directly
related its own capsule. Aide branch ‫ݒ‬ ෝ ௔௜ௗ௘ uses normal
convolution to gather information from capsules located in
other channels. Master and aide branch uses co-efficient
݉௠௔௦௧௘௥ , ݉௔௜ௗ௘ to interact with each other. Co-efficient is
generated by group convolution from both master and aide
branches which are multiplied to each capsule in aide and
master branch.
We propose EncapNet-3D, which is based on EncapNet.
EnCapNet-3D uses single EncapNet-3D module to reduce
parameters. The goal is to achieve close accuracy in just one
module. EncapNet-3D uses 3D convolution to generate co-
efficient. Which is the red block shown in Figure 1. Fast 3D
convolution and succeeded to get higher accuracy than 2D
capsule Network.3D convolution can easily preserve capsule
structure than 2D convolution.
Inputs for 3D convolution and 2D group convolution are
(4x6,128,128) and (4,6,128,128). Both are separated by
groups and have no interaction between channels which avoid
capsules form corruption. The main difference is that 3D
convolution uses 3x3x3 kernel which helps to get the
information of different element of neighbor capsules. 2D
convolution only has 3x3 kernel which can get only
information from same neighbor capsule element which is
 Figure 2 Details of U-EncapNet
placed in same plane. EncapNet uses aide branch to share
information, but 3D convolution generates additional
information about neighbor capsules which helps EncapNet-
3D to achieve higher accuracy. EncapNet only generated co-
efficient per capsule. In order to make master and aide branch
interact more efficient, it is better to generate co-efficient for
each capsule element. Without 3D convolution, capsule
structure will likely collapse. In order to supply capsule
structure to another branch, we used 3D convolution.
EncapNet-3D also uses dropout to reduce overfitting.
EncapNet is very similar to normal CNN because of the
approximate algorithm structured only by the combination of
convolution layers and squash function. The distance between
them can be easily narrowed down by changing the capsule
dimension to 1 which makes capsule a scalar which makes the
network very similar to normal CNN. Changing the channels
to 1 also makes EncapNet very close to normal group
convolution. We propose the learning sequence of stair
learning for EncapNet that gently updates the channels from 1
and gently increasing it to aim parameter helps learning
capsules to learn better. We used normal 2D convolution to
generate feature maps from input image and prediction output
IV. U-ENCAPNET
Encapnet is specialized in classification task. Our
proposed method U-EncapNet uses U-net architecture to
archive high IoU. U-net has achieved high accuracy on
various segmentation tasks. U-net uses encoder-decoder
architecture and skip-connection to supply feature map to
decoder part to support Encoder to get high IoU on
segmentation task. CNN loses precise location information
when feature maps are passed through pooling many times. In
Considering the skip connection between encoder and
decoder, we changed the measuring point of OT loss. OT loss
is one way to describe the divergence of two distributions.
Dynamic routing can be described as optimization problem [7]
and original EncapNet used OT loss as part of approximate
routing. Each block contains dropout layer since U-EncapNet
tends to cause overfitting very easily.
V. EXPERIMENTS
This section shows the experimental results of EncapNet-
3D and U-EncapNet. We explain the dataset used in section
5.A and evaluation results for EncapNet-3D in section 5.B
and U-EncapNet in section 5.C.
A. Dataset
We used two datasets to evaluate our methods. One is a
fluorescence image of the transgenic mice that expressed
fluorescent markers on the cell membrane, cell nucleus and
nucleus [18]. There are 50 images total and the size of the
image is 256 x 256 pixels. We random cropped the image into
128 x 128 pixels and increased the image 2500 total. We
divided the dataset as 2000 for train and 250 for validation
and 250 for test.
Another dataset is segmented anisotropic ssTEM dataset
[12] which has 20 images total and a pixel size of 1024x1024.
It includes membrane, mitochondria, synapses,
glia/extracellular and intracellular classes. We cropped the
dataset and reduced the image size into 512x512 and raised
the image number to 80. We divided the dataset as 60 for train
and 8 for validation and 12 for test. As an evaluation measure,
we used intersection over union (IoU) which is described as
ܶܲ
order to supply location information, U-net concatenated ‘ ൌ ሺʹሻ
feature maps of same layers in encoder together where ܶܲ ൅ ‫ ܲܨ‬൅ ‫ܰܨ‬
where it describes the overlap rate between ground-truth area
location information has not been lost so much.
and predicted area.
Figure 2 shows the structure of U-EncapNet. U-Encapnet
uses EncapNet block at each layer. First 2 blocks do not use
routing. This is because original EncapNet has achieved high
accuracy in ImageNet when first 2 blocks had no routing.

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 Table 1 comparison in cell dataset on EncapNet-3D in average (channel, dim)
Membrane [%] Nucleus [%] Background [%] mIoU [%] parameters(Mb)
EncapNet-3D+MS-dropout(7,6) 42.66 62.81 69.10 58.19 0.741
EncapNet-3D(7,6) 42.08 63.40 70.52 58.66 0.741
EncapNet-3D(6,7) 41.91 63.01 70.64 58.52 0.787
EncapNet-3D-stair(7,6) 42.55 61.88 70.09 58.17 0.741
EncapNet-3D-stair(6,7) 40.37 59.20 69.40 56.32 0.787
EncapNet(7,6) 38.98 58.85 69.31 55.72 0.720
EncapNet(6,7) 38.46 60.73 69.84 56.34 0.773
Resnet-6 41.02 52.25 66.12 53.13 5.006

Table 2 comparison in cell dataset on EncapNet-3D in max (channel, dim)

Membrane [%] Nucleus [%] Background [%] mIoU [%]
EncapNet-3D+MS-dropout(7,6) 43.49 63.07 69.43 58.25
EncapNet-3D(7,6) 43.26 64.86 70.96 59.66
EncapNet-3D(6,7) 43.29 63.98 70.84 59.37
EncapNet-3D-stair(7,6) 44.28 62.90 70.47 58.61
EncapNet-3D-stair(6,7) 41.59 61.29 69.95 57.61
EncapNet(7,6) 39.09 60.24 69.88 56.40
EncapNet(6,7) 40.78 61.43 70.37 57.16
Resnet-6 41.51 53.08 66.63 53.40

Table 3 comparison in ssTEM dataset on EncapNet-3D in average (channel, dim)

Membrane[%] Mitochondria[%] Synapse[%] Glia/Extracellular[%] Intracellular[%] mIoU[%] parameters(Mb)
EncapNet-3D 57.79 45.64 32.19 36.32 89.64 52.32 0.74
EncapNet-2D 59.82 40.79 20.19 34.64 89.85 49.06 0.77
EncapNet 54.04 44.76 29.42 37.76 89.60 51.11 0.72
ResNet-6 62.38 37.97 30.81 32.45 89.67 50.66 0.88
U-Net 70.58 67.63 0.00 36.03 91.78 53.20 39.23

Figure 3 Segmentation results on EncapNet-3D and ResNet-6

compare to original EncapNet. We used only one EncapNet

B. EncapNet-3D block to match the network depth. Similar comparison has
We compare ResNet-6 which uses only one block. been in original EncapNet paper [2]. We also added Dropout
ResNet-6 was chosen to make network depth same. We also which was proposed in MS-CapNet [10] shows that it had

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improvements. Table 1 shows the IoU for the EncapNet-3D.

Figure 4 Segmentation results on EncapNet-3D in ssTEM dataset

Table 4 comparison on U-EncapNet in average

Membrane [%] Nucleus [%] Background [%] mIoU [%] parameters(Mb)
U-Net 47.29 66.88 67.87 60.68 39.23
U-EncapNet 45.26 68.54 71.63 61.81 238.53
U-EncapNet-OT_loss 44.69 68.73 71.91 61.78 238.53
U-EncapNet-OT_loss- 45.87 67.69 71.22 61.59 244.01
U-EncapNet+KL_loss 45.93 68.42 71.56 61.97 238.53

Table 5 comparison on U-EncapNet in max

Membrane [%] Nucleus [%] Background [%] mIoU [%]
U-Net 47.51 67.31 69.02 61.15
U-EncapNet 46.76 69.84 71.84 62.33
U-EncapNet-OT_loss 45.02 68.85 72.09 61.81
U-EncapNet-OT_loss- 47.38 68.34 71.95 62.14
U-EncapNet+KL_loss 46.45 69.30 71.88 62.25

Table 6 comparison in ssTEM dataset on U-EncapNet in average (channel, dim)

Membrane[%] Mitochondria[%] Synapse[%] Glia/Extracellular[%] Intracellular[%] mIoU[%] parameters(Mb)
U-EncapNet 66.50 69.81 30.63 54.55 90.86 62.47 180.42
U-Net 70.58 67.63 0.00 36.03 91.78 53.20 39.23

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All IoU have been measured 3 times and then being averaged.
We can clearly see that all EncapNet-3D exceeds the IoU in
Resnet-6 and original EncapNet. Parameters are very low
compared to ResNet-6. EncapNet-3D-stair which used stair
leaning has higher mIoU than ResNet-6 and original
EncapNet.
Figure 5 segmentation result on U-EncapNet
Figure 6 segmentation result of U-EncapNet in ssTEM dataset
compared to ResNet-6. EncapNet-3D (7,6) has achieved
EncapNet-3D-Capsule-dropout which used Capsule-dropout
only in co-efficient part of the approximate routing has
achieved the highest membrane IoU of all. EncapNet-3D (7,6)
has membrane IoU increase 1.6% and 5.5% in mIoU the
highest mIoU of all in this comparison we can clearly see that
using 3D convolution in approximate routings co-efficient
part helps the EncapNet to achieved better performance in
IoU. Table 2 shows the maximum IoU in EncapNet-3D. This
shows that EncapNet-3D-stair is stronger than EncapNet-3D
in membrane IoU. EncapNet-3D has highest IoU in all expect
membrane. We can see the clear difference between ResNet-
6 which has nearly 3% increase in membrane IoU and 6.2%
increase in mIoU. Figure 3 shows the segmentation results of
EncapNet-3D we can see the clear difference between
EncapNet-3D and ResNet-6.
Table 3 shows that EncapNet has overcome most of the
class IoU other than membrane IoU. Mitochondria class had
7.66% increased in comparison in ResNet-6. EncapNet-2D
which uses 2D group convolution in co-efficient part has
lower mIoU than EncapNet-3D. Capsule Network tends to
struggle with large images because of the huge parameter in
routing, but our proposed method EncapNet-3D successfully
outperforms ResNet-6 and original EncapNet with very little
parameter increase compared to original EncapNet. Figure 6
shows the segmentation results in ssTEM dataset. We can see
that EncapNet-3D has the clearest segmentation image
compared to ResNet-6 and EncapNet.
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C. U-EnCapNet
Table 3 shows the evaluation result of U-EncapNet.
UEncapNet-OT_loss- uses the same measuring point as
original EncapNet. UEncapNet-OT_loss has no OT loss.
UEncapNet+KL_loss uses additional KL_loss at the same
measuring point. We can see that U-EncapNet has about
1.1% increase in mIoU. Changing OT loss has improved
mIoU in 0.1%. U-net has higher membrane IoU but also the
background IoU is lower than U-EncapNet. Table 4 shows
the evaluation result in max. We can see that U-EncapNet has
small difference between average and max.
Table 6 shows the evaluation results in ssTEM dataset. We
shrunk the network filter size in order to fit in one GPU. We
can see that U-EncapNet has 2.2% increased in comparison
in Glia/Extracellular class. U-EncapNet also has 18.52%
increased in comparison with U-net in Synapse class which
tends to be small. Figure 4 shows the segmentation results
from U-EncapNet. We can clearly see that U-net has thick
membrane to get higher membrane IoU. U-EncapNet has
thinner membrane which is more difficult to get higher
Membrane IoU because in order to get a thin membrane and
achieve a high membrane IoU at the same time needs precise
location information. Capsule network preserves the location
information which makes it possible to achieve this.
Figure 7 shows the segmentation result of U-EncapNet. We
can see that U-EncapNet has thinnest cell membrane of all.
By the segmentation results of cell image dataset and ssTEM
dataset, U-EncapNet tends to predict thinner membrane
compared to U-net.
D. Consideration
Looking at Table 1 and Table 4, mIoU has about 3.31%
difference and membrane IoU has about 4.62% difference,
but comparing Table 2 and Table 4 narrows the difference
between U-EncapNet and EncapNet-3D to 3.2% in
membrane IoU and 2.6% in mIoU. Considering the
parameters of EncapNet-3D, it has achieved very low
performance decrease.
Looking at Table 3 and Table 6, We can see that EncapNet-
3D and U-net has only 0.88% difference in mIoU and has 52
times smaller network parameter in comparison in U-net. We
successfully got very close accuracy in EncapNet-3D
comparted to U-net. This dataset was huge and is challenging
for capsule network because not so many has succeeded to
deal with large image input like 512x512 in capsule network
VI. CONCLUSION
In this paper, we proposed EncapNet-3D, which uses 3D
convolution for co-efficient parameter in master, aide branch
of approximate routing. EncapNet-3D had successfully
achieved very close accuracy with only one block in some
class IoU in semantic segmentation compared to U-net in cell
image dataset and ssTEM dataset. We reduced the network
parameters to 52 times smaller than U-net.
We also proposed U-EncapNet, which is EncapNet that
uses U-net architecture. U-EncapNet had successfully
outperformed U-net in most class IoU on cell image dataset
and ssTEM dataset.
However, both networks had difficulty achieving high
accuracy in membrane IoU in both datasets. U-EncapNet had
thinner membrane which is more difficult to achieve high
accuracy than U-net which had thick membrane. EncapNet-
3D on other had higher cell membrane IoU than ResNet-6 in
cell image dataset but it had difficulty in ssTEM dataset. In
future, we would like to improve the accuracy of cell
membrane by improving the approximate routing of an
EncapNet-3D.
ACKNOWLEDGMENT
This work is partially supported by MEXT/JSPS
KAKENHI Grant Number 18H04746 "Resonance Bio".
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