Computer Aided Kidney

Stone Diagnosis and

treatment planning based
on 3D CT Images

Presented by
Ma Lai Yee Myint
Ph.D CEIT – 5 (13th Batch)
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Introduction
• Kidney Stones are small, hard deposits of mineral and acid
salts on the inner surfaces of the kidneys (drops along the
urinary track).

• Alternative names include:

• Nephrolithiasis
• Urolithiasis
• Ureterolithiasis

http://www.pilotfriend.com/aeromed/medical/images2/25.jpg
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 Background
• Why doing research in Kidney Stone Disease?
– Prevalence of kidney stone disease and recurrence rate
Lifetime prevalence of incident kidney stones in the United

10.0%
8.8%
9.0%
8.0%

7.0%
6.0% 5.2%

5.0%

4.0% 3.2%

3.0%

2.0%
1.0%
States

0.0%

Fig: Prevalence of kidney stone disease from 1976 to 2010 [1] Fig: Recurrent rates of kidney stone forming after treatment [1]

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 Background
• GBD(GLOBAL BURDEN OF DISEASES) 2010
– Years of life lost (YLLs) quantify premature mortality in Myanmar [2][3]
Chronic Kidney Disease in period of 20 years (from 1990 to
2010)
1.80%
1.60%
1.40%
1.20%
1.00%
0.80%
0.60%
0.40%
0.20%
0.00%
1990 2010

% of total disease

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 Related Researches Advantage Limitation
An artificial intelligence-based clinical Predict treatment procedure (stent Using patient history variable,
Previous Works
decision support system for large kidney
stone treatment [4].
place after stone removal, blood kidney stone parameters and
transfusion during the surgery or not) laboratory data

S.T.O.N.E. Nephrolithometry: Novel Surgical Predict only PCNL treatment success Using stone parameters: stone size
Classification System for Kidney Calculi [5] or the risk of perioperative (S), tract length (T), obstruction (O),
complications after PCNL number of involved calices (N), and
essence or stone density (E)

Measuring stone volume - Three-dimensional Classify: Small, Medium and Large No single formula for estimating
software reconstruction or an ellipsoid stone stone volume
algebra formula? [6]
Predicting shockwave lithotripsy outcome for Predict the probability of stone free Using patient history variable,
urolithiasis using clinical and stone computed outcome after ESWL treatment kidney stone parameters
tomography texture analysis Variables [7]

Kidney Stone Diagnosis and Management [8] Predict treatment type Using linear measurement of stone
1. Based on HU value (* inappropriate in irregular stone,
2. Based on size eg: staghorn calculi)
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Contribution

Stone
density
Stone size
(only HU
value)

Surgical Management of Urinary Lithasis, by MohammadBaghdadi,

Urology resident KKNGH, https://slideplayer.com/slide/1570041/
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 Contribution
Previous work New contribution

• Stone size & density (only HU value) • More than two parameter
• Stone parameter using CT, (size & density)
Stone size/length, Area(total no. of pixels) and Mean HU • Stone parameters of each
were measured from the largest cross-sectional slice of stone in a patient are
the largest stone where more than one stone was measured based on 3D (Not
treated. Stone volume is the sum of individual stone only one slice)
volumes in cases with more than one stone • Decide the treatment type
• Completely depend on radiologist • Fully automated computer
aided system

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 Problem formulation

Failure in some kidney stone cases

Spreading of kidney stone in the urinary system (kidney,
ureter and bladder )
Bone

Consisting of stent, calcification, bone fragment together Stent

Stone

with stone
(appear on CT_ bright-white appearance similarity,
variety of size, shape, intensity and location) Calcification

Consisting of one or more types of stone in each patient

(appear on CT_ bright-white appearance similarity,
variety of size, shape, intensity and location)

R. Ray, R. Mahapatra, P. Mondal, and D. Pal, “Long-term complications of JJ stent and its management: A 5 years review,” Urol. Ann., vol. 7, no. 1, p. 41, 2015.
8 pp. 268–
H. J. Lee et al., “Differentiation of urinary stone and vascular calcifications on non-contrast CT images: An initial experience using computer aided diagnosis,” J. Digit. Imaging, vol. 23, no. 3,
276, 2010.
 Problem Statement

Failure in some kidney stone cases

Difficulty to distinguish the stone among other high-intensity objects (stent,

calcification, bone fragment)

Difficulty to diagnose the kidney stone problem and to make medical treatment
decisions without the help of expert person

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Objective

To obtain all kidney stones in the urinary system simultaneously

without any other unwanted regions

To provide the essential information and 3D visualization for

diagnosis and treatment planning without any other expert
persons
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 Proposed Methods
Treatment
Planning

False Positive • Conditional

• Thresholding Reduction
statement
and Otsu’s • Geometric
(IF-THEN-ELSE)
method Features (Area,
• Morphological • Geometric Size, Volume,
operation feature-based Density)
thresholding • Iso-surface
generation
techniques
using
3D Segmentation Marching
(Noise Removal) 3D Feature Extraction Cubes
Algorithm
3D Visualization
for diagnosis
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 Thresholding and Otsu’s Method
• Thresholding:
– Simplest methods for image segmentation
– Assign _ every pixel above a defined intensity (threshold value) as one type of region (foreground),
whereas every pixel below that intensity as another type of region (background).
– Two types of thresholding :
• Global Thresholding: only one threshold value for entire image
• Local Thresholding: different value for different regions
• Otsu’s Method
– Used to find the threshold value for segmentation
– Based on selecting the lowest point between
two classes (peaks).

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 Morphological operations
• Morphological operation:
– A broad set of shape-based image processing operations.
– The value of each pixel in the output image is based on a comparison of the corresponding
pixel in the input image with its neighbors. By choosing the size and shape (Circular disks,
crosses, diamonds, lines and squares etc.) of the neighborhood, a morphological operation can
be constructed that it is sensitive to specific shapes in the input image.
• Four basic morphological operations
– Morphological Dilation : to fill holes and close gaps in lines
– Morphological Erosion : for shrinking an object in the image and removing isolated pixels
– Morphological Opening : application of erosion followed by dilation (used to remove small
objects)
– Morphological Closing : application of dilation followed by erosion (used to close small holes
in an objects) 13
3D Segmentation (Noise Removal)

• Low_intensity region removing

– Intensity-based thresholding method
• Unneeded high_intensity region removing
– Size-based thresholding method

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Intensity-based thresholding method

 In step 1, Two constant threshold values, and (200

HU and 2800 HU values )
 Step 2, foreground and background are segmented
into two groups of pixels and , using and :
(1)
 Step 3, finally, the new image is outputted with,
after eliminating group.
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Size-based thresholding method

 Step 1, Calculate the size (longest diameter )of each object

through the bounding box calculation in [9].
 Step 2, Two constant threshold values, and (3mm and 50 mm)
[10].
 Step 3, Foreground and background are segmented into two
groups of pixels and without using, and
(2)
 Step 4, Finally, the new image is outputted with , after
elimination group.
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False-positive reducing

• Volume and average HU values -based thresholding

method

* One of new contribution of the research

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Volume and average HU values -based thresholding method

 Step 1, Calculate the required threshold values ( and ) using following equation, and
regarded with 0.03 and 35 as consideration of the relationship between volume and
HU of kidney stone.


– is the average HU for each object, n is the number of voxels in an object. µ is the HU value of each voxel in an object.

 Step 2, Segment the image into two groups of pixels and without using, and
•
 Step 3, Develop the new image with , after elimination group.
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 Experiment Results
 Working on 551 CT slices of a patient, our experiments
demonstrated that the proposed algorithm is removed unwanted
surrounding objects step by step.

2D Slide mode of 3D Volume mode of Result of after Low_intensity

original DICOM original DICOM image region removing
image 19
Experiment Results

Result of after Unneeded high_intensity Result of after false positive removing

region removing
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Results Analysis 1
• After loading 500-600 slices of each patient, it is constructed the original image which consists of
over 500000 labels.
• In the first process, the algorithm can remove all regions having hypodense and isodense structure
from the abdomen CT image and reduce the unwanted objects up to 4300 labels on average from
over 500000 labels.
• In the second process, hyperdense region removing, the algorithm removes the bony skeleton, bed
mat, and some bones but the average of the remaining labels is about 112.
• The final output is clear in visualization and remains only an average of 21 labels in an image.
• So, it can remove most of unwanted objects.

Hypodense and isodense region Hyperdense region removing False-positive reducing

removing
4300 labels 112 labels 21 labels

Table 1. Average Result of All 50 Patients in Each Process 21

Results Analysis 2


 where, TP and FN are used for kidney stones which are correctly detected and not detected in system,

TP FN Sensitivity
66 3 95.7%

Could carry out the unneeded regions removing with a significant stone detecting.

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Outcomes
• The proposed method, unwanted region removing, gives good support in kidney
stone detection, and correctly remove the unneeded region and provide the
output image in a clear form.
• Because of using thresholding methods based on the nature of kidney stones on
CT imaging, the proposed scheme is simple and easy to understand for kidney
stone classification.
• The result is good and satisfactory.
• According to the analysis, the proposed model could detect the kidney stones
with 95.7% in sensitivity.
• Therefore, the performance of the proposed scheme is effective and efficient
with good sensitivity.
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Geometric Features

Area
• Area=Total number of voxel in the selected region

Volume
• Volume = area of object × voxel resolution (voxel spacing)
Size
• Diagonal, high, width

Density
• Average HU in periphery region , Average HU in core region , Core-periphery HU variation
• Density = Average Hu / diameter (Based on the largest slice of the object) Next progress
System Design

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Expected Benefits of research

To be a good assist for urologist in making medical decision

Speed up the diagnosis process

(By giving the size, density and 3D visualization)

Decide the right treatment decisions

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Future Work

• will focus on density to estimate treatment type

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 References
[1] M. S. C. Morgan and M. S. Pearle, “Medical management of renal stones,” Bmj, vol. 2005, p. i52, 2016.
[2] YLDs, “WHO-Health metrics_GBD profile: Myanmar,” vol. 2010, no. Gbd, pp. 1–4, 1990.
[3] “SUPPORT LIFE EXPECTANCY RESEARCH!,” WORLD HEALTH ORGANIZATION 2017, 2017. [Online]. Available:
http://www.worldlifeexpectancy.com/myanmar-kidney-disease.
[4] Shabaniyan, T., Parsaei, H., Aminsharifi, A. et al. An artificial intelligence-based clinical decision support system for large kidney stone treatment.
Australas Phys Eng Sci Med 42, 771–779 (2019). https://doi.org/10.1007/s13246-019-00780-3
[5] Zhamshid Okhunov, M.D., Arvin K. George, M.D., Arthur D. Smith, M.D., and Zeph Okeke, M.D., Arthur Smith Institute for Urology, Hofstra North
Shore-Long Island Jewish School of Medicine, New Hyde Park, New York http://dx.doi.org/10.1016/j.urology.2012.10.086
[6] W. Finch, R. Johnston, N. Shaida, A. Winterbottom, and O. Wiseman, “Measuring stone volume - Three-dimensional software reconstruction or
an ellipsoid algebra formula?,” BJU Int., vol. 113, no. 4, pp. 610–614, 2014.
[7] HelenW. Cui, Mafalda D. Silva, AndrewW. Mills, BernardV. North and BenjaminW.Turney, “Predicting shockwave lithotripsy outcome for
urolithiasis using clinical and stone computed tomography texture analysis variables,” Natureresearch, 11 October 2019.
[8] Dushyant V Sahani, MD, “Kidney Stone Diagnosis and Management.,” Department of Radiology, Massachusetts General Hospital., vol. 27, no. 2,
pp. 162–7, 2013.
[9] M. Vallières, C. R. Freeman, S. R. Skamene, and I. El Naqa, “A radiomics model from joint FDG-PET and MRI texture features for the prediction of
lung metastases in soft-tissue sarcomas of the extremities,” Phys. Med. Biol., vol. 60, no. 14, pp. 5471–5496, Jul. 2015.
[10] C. D. Scales, A. C. Smith, J. M. Hanley, and C. S. Saigal, “Kidney Stones in Adults,” NIH Publ., vol. 13, no. 2495, pp. 160–165, 2012.

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Published Paper

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THANK YOU VERY MUCH FOR
YOUR ATTENTION !!

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