Computer Vision Based Estimation of Shrimp
Population Density and Size
Trung Thanh N. Thai 1,2 Thanh Sang Nguyen 1,2
1Ho 1Ho
Chi Minh City Uni. of Technology Chi Minh City Uni. of Technology
2Vietnam National University HCM 2Vietnam National University HCM
thanh.thai.nt@hcmut.edu.vn tsang0949@gmail.com
Abstract—Shrimp is one of the most important aquaculture
products in Vietnam and it is desired to continuously estimate
shrimp population density and size. This paper presents our initial
steps in supervising aqua farming based on computer vision
techniques. The computer vision system includes U-net
segmentation, marker-controlled watershed segmentation,
thresholding, contour tracing, etc. Experiment results show that
the proposed method can obtain good results in counting shrimps
(mean absolute error of 0.093) and estimating shrimp lengths
2021 International Symposium on Electrical and Electronics Engineering (ISEE) | 978-1-6654-1487-6/21/$31.00 ©2021 IEEE | DOI: 10.1109/ISEE51682.2021.9418638
(RMS error of 0.293 cm) when they are separately located.
Keywords— shrimp farming, computer vision, deep learning,
U-Net, watershed segmentation
I. INTRODUCTION
Tracking the sustainability of aquaculture population is
highly desirable but challenging. It is well known that cultured
shrimps are vulnerable to environmental changes that can
cause mass deaths leading to severe losses of farmers. In
Southern Vietnam especially in the Mekong Delta region,
natural farming conditions have become more and more
severe due to saltwater intrusion and climate change. Shrimp
farming in Vietnam was reported suffering a considerable
decrease in production and mass export in the first ten months
of 2019, in comparison with that of 2018. To support shrimp
farming, it is desirable to continuously supervise and timely
feedback statistics of the aquaculture population to help
farmers making right decisions.
Computer vision techniques have been applied to the field
of shrimp farming. In [1], a highly sensitive underwater video
system was developed to obtain high-quality videos and
images in turbid, low-light aquafarming ponds. The system
can be utilized for monitoring shrimp feeding, evaluating
shrimp size, shrimp health, and excess organic matters. In [2],
a model of a smart underwater monitoring system was
proposed to control feeding and to manage water quality based
on underwater observation and analysis. The system can
detect shrimp and shrimp food however the detection accuracy
was not discussed.
This paper presents our initial steps in supervising shrimp
farms based on computer vision techniques. In particular, a
computer system is built to capture and analyze images of
shrimps to estimate shrimp population density and
individual’s length.
II. METHODOLOGY
The proposed solution comprises three parts. First, images
of shrimps are captured and transferred to a processing
computer. A computer vision system, including U-net
segmentation, watershed segmentation, thresholding, contour
finding, etc., is then utilized to count shrimps and to estimate
shrimp length. Finally, a friendly web interface was
established to provide an easy and efficient usage of the
system.
978-0-7381-3196-2/21/$31.00 ©2021 IEEE
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Viet Cuong Pham1,2
1Ho
Chi Minh City Uni. of Technology
2Vietnam National University HCM
pvcuong@hcmut.edu.vn
Flowchart of the computer vision system is given in Fig. 1.
Images captured from shrimp ponds are first processed by the
U-net segmentation technique to obtain greyscale images.
Resulting images are then processed by the marker-controlled
watershed segmentation to improve the segmentation,
especially in cases of touching/overlapping shrimps.
Thresholding technique is then used to extract shrimps.
Finally, contours and bounding boxes are found to count
shrimps and to estimate shrimp length.
Fig. 1. Flowchart of the computer vision system.
A. U-Net segmentation
U-Net [3] is a well-known segmentation method which
won the IEEE International Symposium on Biomedical
Imaging cell tracking challenge in 2015. It is a fully
convolutional network that can assign a class label to each
pixel of an image. It is claimed to be able to work well even
with a small dataset.
The network has a U sharp with 23 convolutional layers,
including a contracting path and an expansive path. The
contracting path has an architecture similar to that of a
convolutional neural network, consisting of repeated blocks of
two 3×3 convolutions, each followed by a rectified linear unit
(ReLU) and a downsampling 2×2 max pooling block with a
stride of 2. The number of feature channels is doubled at each
downsampling step. Every step in the expansive path consists
of an upsampling of the feature map followed by a 2 × 2
convolution that halves the number of feature channels, a
concatenation with the correspondingly cropped feature map
from the contracting path, and two 3×3 convolutions, each
followed by a ReLU. A 1×1 convolution is used at the final
layer to map each 64-component feature vector to the desired
number of classes.
Our dataset includes 181 images collected from the
laboratory environment in which 100 images were used for
training and the rest for testing. For each image in the training
set, binary masks are manually created as shown in Fig. 2. Data
augmentation technique was used to enrich the training
dataset.
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Fig. 2. Training data including original images and manually labeled binary
masks.
Fig. 3. Binary mask (left) and result after implementing Euclidean distance
B. Marker-controlled Watershed Segmentation calculation algorithm (right).
For shrimps touching or overlapping each other, U-net
Markers are then found as shown in Fig. 4 while result after
tends to recognize them as one segment. To deal with this
using thresholding technique is illustrated in Fig. 5. Finally,
situation, the marker-controlled watershed segmentation is
contours and bounding boxes are found to count shrimps and
employed. Marker-controlled watershed segmentation
to estimate shrimp lengths.
algorithm has been shown to be a robust and flexible method
for the segmentation of objects with closed contours, where
the boundaries are expressed as ridges. The marker image
used for watershed segmentation is a binary image consisting
of single marker points or marker regions, where each
connected marker is localized inside an object of interest.
After segmentation, the boundaries of the watershed regions
are arranged on the desired ridges separating each object from
its neighbors.
The marker-controlled watershed segmentation algorithm
is as follows:
Fig. 4. Masks (left) and markers (right, markers are magnified for
• Step 1: Assign a unique label to each minimum. illustration).
Initialize set S of labeled points, V contains
watershed lines (V is empty initially).
• Step 2: Insert unlabeled neighboring pixels in the Q
priority queue, sorted by grayscale value.
• Step 3: Take pixel x from the top of the queue Q
follows by: F(x) = min{F(y) | y ∈ Q}: If x is adjacent
to a labeled region, we label x by that region (with
the same label), and add it to S, then add the
unlabeled neighbors to queue Q.
• Repeat Step 3 until Q is empty.
The number of markers equals the number of watershed Fig. 5. Input grayscale image on the left with thresholded image on the right
regions thus each marker has a one-to-one mapping to a
particular watershed region. The markers can be manually or III. WEB-BASED SHRIMP FARMING MONITORING
automatically selected, but automatically generated markers Heroku, developed since 2007, is a cloud computing
are preferred. Markers can be created by various methods. In service supporting several programming languages [5, 6].
the paper, the Euclidean distance calculation algorithm [4] is Heroku is considered as a polyglot platform thanks to its
employed where value of each pixel is replaced with its supporting developers to build and run applications in a
Euclidean distance to the nearest zero-value pixel (x0, y0) (the similar manner across most languages.
nearest background pixel) as shown in Fig. 3, calculated by:
After submitting some required parameters, the
, application does the processing job at Heroku server-side
where all the algorithms are deployed, then displays the
farming specifications which include shrimp lengths and
shrimp of population density as shown in Fig. 6.

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Fig. 6. One of our ultimate results displayed on web application

IV. EXPERIMENTAL RESULTS

The proposed method was evaluated on its capability of
counting shrimps and estimating shrimp lengths. The shrimp
counting ability is assessed on 81 images collected from our
laboratory environment. Each image contains from one to
four shrimps. The total number of shrimps in those images is
175. Some typical images are shown in Fig. 7.

Fig. 8. Correct estimation of shrimp number in an image.

Fig. 9. Underestimation of shrimp number in an image.

The system is quite robust in segmenting small parts of

shrimps as shown in Fig 10. As can be seen, a small part of a
shrimp, almost only the tail, can also be correctly segmented.

Fig. 7. Typical images captured from laboratory environment.

Among 81 test images, there are 59 images containing

only one shrimp or separately located shrimps as illustrated
in Fig. 7. For those images, the proposed method performs
well in counting shrimp with mean absolute error of 0.093
(error of 11 over 118 shrimps). Most of the time (50/59
images) the method counted exactly the number of shrimps
in images, sometimes (9/59 images) it under-estimated the
number of shrimps. Some results are illustrated in Fig. 8 and
Fig. 9. Fig. 10. Correct segmentation of small parts of shrimps.

For the remaining 22 images containing shrimps

touching or overlapping each other (besides
touching/overlapping shrimps, those images may also contain
other separately located shrimps) as illustrated in Fig. 11, the
proposed method often counted two touching/overlapping
shrimps as one as shown in Fig. 12 thus the mean absolute error
in this case is 0.298 (error of 17 over 57 shrimps). The overall
mean absolute error for all 81 images is 0.160 (error of 28
over 175 shrimps).

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Fig. 11. Images with shrimps touching or overlapping each other.
Fig. 12. Segmentation result for images with shrimps touching or
overlapping each other.
The capability of shrimp length estimation was also
evaluated. Shrimp lengths were first determined by using a
tap measure (Fig. 13) then they were estimated by the proposed
method (Fig. 14). The average length of shrimps used in this
assessment is 14.92 cm. The root mean square error is 0.293
cm.
Fig. 13. Manual measurement of shrimp length.
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Fig. 14. Estimation of shrimp length.
V. CONCLUSIONS
This paper presents our initial steps in solving the
problem of shrimp farming supervision based on computer
vision. The proposed method, utilizing U-net and watershed
segmentation techniques, can estimate shrimp length and
count shrimps well when they are separately located.
However, its performance degrades when shrimps are
touching or overlapping each other. Object detection
approach will be investigated to deal with this challenging
situation.
ACKNOWLEDGEMENT
We would like to thank Ho Chi Minh City University of
Technology (HCMUT), VNU-HCM for the support of time
and facilities for this study.
REFERENCES
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August 2016.
[2] Ing-Jer Huang, Chin-Chang Hung, Shiann-Rong Kuang, Yun-Nan
Chang, Kuan-Yu Huang, Chang-Ru Tsai and Kai-Lin Feng, “The
Prototype of a Smart Underwater Surveillance System for Shrimp
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[3] Olaf Ronneberger, Philipp Fischer, and Thomas Brox, “U-Net:
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[4] Ivan Dokmanic, Reza Parhizkar, Juri Ranieri and Martin Vetterli,
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[6] “About Heroku”, Stack Overflow, Retrieved March 2016.
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