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OPEN A high-quality dataset featuring

Data Descriptor classified and annotated cervical
spine X-ray atlas
Yu Ran1,9, Wanli Qin 2,9, Changlong Qin3,9, Xiaobin Li4, Yixing Liu5, Lin Xu6, Xiaohong Mu6,
Li Yan7, Bei Wang1, Yuxiang Dai8, Jiang Chen6 ✉ & Dongran Han1 ✉

Recent research in computational imaging largely focuses on developing machine learning (ML)
techniques for image recognition in the medical field, which requires large-scale and high-quality
training datasets consisting of raw images and annotated images. However, suitable experimental
datasets for cervical spine X-ray are scarce. We fill the gap by providing an open-access Cervical Spine
X-ray Atlas (CSXA), which includes 4963 raw PNG images and 4963 annotated images with JSON
format (JavaScript Object Notation). Every image in the CSXA is enriched with gender, age, pixel
equivalent, asymptomatic and symptomatic classifications, cervical curvature categorization and 118
quantitative parameters. Subsequently, an efficient algorithm has developed to transform 23 keypoints
in images into 77 quantitative parameters for cervical spine disease diagnosis and treatment. The
algorithm’s development is intended to assist future researchers in repurposing annotated images for
the advancement of machine learning techniques across various image recognition tasks. The CSXA
and algorithm are open-access with the intention of aiding the research communities in experiment
replication and advancing the field of medical imaging in cervical spine.

Background & Summary

Cervical spine diseases are recognized as a public health issue, characterized by diversity and high morbidity,
which contained mainly cervical spondylosis, malformations, fractures, instability, and spondylolysis1,2. Over
a third of a billion people suffered from persistent mechanical neck pain for at least three months, as indicated
by a global assessment in 20153. X-ray is a common and cost-effective method to evaluate cervical spine dis-
eases, especially in screening and follow-up4,5. It is imperative for post-operative assessment in Anterior Cervical
Corpectomy and Fusion (ACCF), Anterior Cervical Discectomy and Fusion (ACDF), and Anterior Cervical
Disc Replacement (ACDR)6.
Quantitative parameters in X-ray imaging serve as the critical content of assessment for cervical spine dis-
eases7. In routine clinical practice, surgeons primarily rely on manual measurements or visual assessments,
with disparities in professional expertise contributing to an elevated risk of misdiagnosis and measurement
inaccuracies. The results of manual measurements are usually obtained by taking the average of measurements
from multiple surgeons. Nevertheless, this time-consuming and labor-intensive method lacks cross-checking8.
Thus, failing to reduce the subjective impact of surgeons and unable to mitigate inherent errors associated with
manual measurements. Moreover, the vast array of quantitative parameters for cervical spine disease assessment
are extremely difficult to be obtained by manual measurement.
Machine learning (ML) can assist and replace manual efforts in performing extensive and precise complex
calculations. Nevertheless, ML requires large-scale and high-quality training datasets consisting of raw images

1
School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China. 2Department of
Dermatology, Air Force Medical Center, Air Force Medical University, Beijing, 710000, China. 3Department of
Orthopedics and Traumatology, Qiannan Traditional Chinese Medicine Hospital, Guizhou, 558000, China. 4Shenzhen
Hospital of Beijing University of Chinese Medicine, Shenzhen, 518172, China. 5School of Management, Beijing
University of Chinese Medicine, Beijing, 102488, China. 6Department of Orthopedics, Dongzhimen Hospital,
Beijing University of Chinese Medicine, Beijing, 100700, China. 7School of Humanities, Beijing University of Chinese
Medicine, Beijing, 102488, China. 8Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai,
200032, China. 9These authors contributed equally: Yu Ran, Wanli Qin, Changlong Qin. ✉e-mail: dr.jiangchen@
foxmail.com; [email protected]

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and annotated images. Presently, the publicly accessible large X-ray datasets predominantly encompass chest
radiographs and fractures, with a portion of the studies incorporating merely classification data, thus lacking
annotations requisite for quantitative analysis9–13. Existing datasets of cervical spine X-rays, which amalgamate
images of the cervical, thoracic, lumbar, and whole spine14, exhibit considerable variability stemming from the
distinct anatomical structures of the vertebral body and their unique physiological and pathological character-
istics. Such marked differences in data characteristics significantly limit their suitability for machine learning, as
the heterogeneity hampers the consistent application required for effective algorithmic training. Additionally,
previous datasets present problems with small sample size, inconsistent image clarity, or are primarily used for
reclassification tasks based on existing datasets (instead of creating a new dataset). Evidently, suitable datasets
for cervical spine X-ray are scarce. To fill the gap, we developed Cervical Spine X-ray Atlas (CSXA), a dataset
specifically and meticulously designed for the application of ML in the realm of cervical spine imaging.
Ensuring the quality of image annotations is crucial for the integrity of the entire dataset. Image annotations
play a key role not only in machine learning applications but also essential for algorithms focused on measuring
quantitative parameters. These quantitative parameters are derived from the annotations of vertebral keypoints,
including the four corner points and the centroid of each vertebra15,16. This allows us to compute quantitative
parameters from the keypoints in image annotation. The annotation of keypoints is full of challenges in specific
images of vertebral body ghosting, defects, artifacts, bone hyperplasia, and osteoporosis, which are retained in this
dataset to generate a robust and generalizable ML model. Non-specialist orthopedic spine surgeons often struggle
with accurate image annotation. Therefore, image annotation of keypoints was independently performed by four
orthopedic spine surgeons with an average of 6 years of experience (range 3–12), and was cross checked three times.
The algorithm based on keypoints addresses the issues of laborious manual processes, measurement errors, lack
of cross-checking, and incomplete parameters measurement17. However, quantitative parameters for diagnosing
cervical spine diseases are actual distances, while algorithmic outputs are pixel values. A previous study adopted16
the ratio of distances within images due to the challenges in acquiring pixel equivalent. Pixel equivalent18, defined
as the ratio of actual distance to pixel distance, plays a crucial role in converting a part of parameters in the study of
cervical spine X-ray. It is essential to establish the relationship between pixel and physical dimensions to accurately
translate these into actual distances and areas. In this study, we meticulously computed for each image with Python
scripts by dividing the pixel values of the scale in each image by the corresponding graduated markings.
The CSXA, algorithm and basic information are open-access with the intention of aiding the research com-
munities in experiment replication and advancing the field of medical imaging in cervical spine (Fig. 1).

Methods
Medical ethics. The ethics committee of Dongzhimen Hospital of Beijing University of Chinese Medicine
approved this study (Ethical approval number: 2024DZMEC-126). Cervical spine X-rays removed any identifia-
ble information except for gender and age, and other data underwent secondary processing based on these X-rays
to protect patients’ privacy. We received an exemption from individual informed consent, as obtaining informed
consent would hinder the study.

Image annotation. Image annotation toolImage annotation of keypoints was independently performed by four
orthopedic spine surgeons who had an average of 6 years of experience (range 3-12), and was cross checked
three times. The cross-checking labels were referred to a senior orthopedic spine surgeon with over 12 years
of experience for the final review and validation. All data were annotated using the labelme plug-in (pip install
labelme) from Anaconda Powershell Prompt (Anaconda3) in ANACONDA (https://www.anaconda.com).

Selection of keypoints. Keypoints selection is foundational to subsequent analyses in cervical spine X-ray stud-
ies. Selected keypoints include the inferior endplate of C2, the central point of C2, and the corners of C3-C7
vertebrae, which are extensively used to generate diagnostic parameters, encompassing a wide range of lines and
angles. The algorithm is designed for parameter calculations, characterized by its objectivity, reproducibility,
and accuracy. It increases the number of keypoints and performs essential parameter calculations based on these
keypoints. The upper endplate of the C2 (axis) vertebra and the C1 (atlas) were not selected due to their unique
osseous connections and the absence of an intervertebral disc, which create unclear boundaries on X-rays. This
method of keypoint selection and annotation is particularly well-suited for the quantitative analysis and classi-
fication of cervical spine diseases.

Naming of keypoints. Every annotated JSON image contains 23 keypoints, which are annotated using differ-
ent colors by the labelme. The color and name of the keypoints of every image are consistent. The keypoints
include the four corner points of the third to seventh cervical vertebral body (C3 to C7), and the central point
and the two corner points of lower endplate of C2. The corner points are the four intersections which formed by
the upper and lower endplates of the vertebral body with the anterior and posterior edges. The keypoints were
named as indicated in the legend to Fig. 2.

Cross-checking of keypoints. Researcher 1, with three years of experience, initially annotated all 4,963 images.
Researcher 2, also with three years of experience, reviewed the annotations and selected images requiring mod-
ifications, passing on the remaining, unselected images to Researcher 3. Researcher 3, With six years of expe-
rience, reviewed the transferred images and again selected those needing further modifications, forwarding
the rest to Researcher 4. Researcher 4, with twelve years of experience, performed the final individual review,
selected additional images for modifications. Finally, the images selected by Researchers 2, 3, and 4 as needing
modifications were reviewed and discussed by all four researchers to finalize the amendments.This sequential

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Fig. 1 The flowchart for creating the CSXA dataset: (1) Image A illustrates the construction of the raw image
of cervical spine X-ray. (2) Image B shows the naming of the keypoints, as well as the naming of the raw images
and annotated images. (3) Image C depicts the methods of image annotation and cross-checking. (4) Image D
is a schematic diagram illustrating the calculation of pixel equivalent. (5) Image E demonstrates the main
algorithms used for converting annotated images into quantitative parameters. (6) Image F presents the
complete data of the CSXA dataset, including 4963 raw and annotated images, two types of codes, and data
about all basic information and quantitative parameters.

and multi-tiered screening process effectively harnesses the expertise of different researchers and ensures the
high quality of annotations.

Picture naming. The preceding four digits represent the image’s sequence number with a range from 0001 to
5000 in the CSXA, and the fifth digit is the gender code (1 for female, 0 for male). The final two digits are the
age (ages 10 and above are represented directly; ages below 10 are indicated with a leading 0). The names of raw
images are the same as the corresponding annotated JSON files (Fig. 3).

Population classification. The CSXA consists of two population groups: asymptomatic individuals and symp-
tomatic patients. The inclusion of asymptomatic participants was from individuals undergoing health checkups
for personal reasons at the International Department of Dongzhimen Hospital, affiliated with Beijing University
of Chinese Medicine. Symptomatic persons are included individuals visiting at Dongzhimen Hospital, Beijing
University of Chinese Medicine.

Doctor label of cervical curvature. According to the Modified Toyama19 cervical curvature classification, the
cervical curvature is classified into four groups: Lordotic group, Straight group, Sigmoid group, and Kyphotic
group. Interestingly, during our manual sorting of images, we discovered that the Sigmoid group in the Modified
Toyama classification can be further divided into two main subtypes. We classified the posterior convexity of the
C3 and C4 vertebral body as Sigmoid 1, and the posterior convexity of the C5 and C6 vertebral body as Sigmoid 2.

Quantitative parameters based on keypoints data analysis:

1. Disc height20: The vertical and straight-line distance between the corner points of two adjacent vertebral
bodies (Fig. 4A,D);
2. Vertebral body16: The straight-line distances of the anterior and posterior sides, as well as between the
superior and inferior endplates of a vertebral body, are measured between the corner points (Fig. 4A);
3. Cervical disc angle21 (CDA): The CDA was defined as the angle formed by the endplates of the upper and
lower vertebral bodies (Fig. 4B). Furthermore, a classification with positive on the posterior side of the verte-
bral body and negative on the anterior side was provided to meet the needs of different research communities.

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Fig. 2 Fully tagged and labelled sample image.

0101120 0101120

Fig. 3 Schematic diagram of picture naming. ‘0101120’ denotes the 101 sample, a 20-year-old female.

4. Functional Spinal Unit22 (FSU): FSU consists of an upper and a lower vertebra with an intact intervertebral
disc (Fig. 4C), and a classification with positive on the posterior side of the vertebral body and negative on
the anterior side.
5. Parameters of cervical spine instability23: Radiologic diagnosis of instability is the angle of adjacent ver-
tebrae greater than 11 degrees or anterolisthesis greater than 3.5 mm of one vertebral body on another. In
fact, the angle between adjacent vertebrae is CDA. The anterolisthesis is the anterior-posterior distance
of the corner points of adjacent vertebral bodies on a horizontal line. If the upper vertebra is to the left of
the lower vertebra, it is counted as a positive number, and if to the right, as a negative number; calculate
separately for the anterior and posterior edges of the two adjacent vertebral bodies (Fig. 4D).
6. Vertebral body slope24: C2 slope is defined as the angle between a line parallel to the lower endplate of
the C2 vertebra and the horizontal plane. C3, C4, C5, C6, and C7 slope are defined as the angle between
a line parallel to the upper endplate and the horizontal plane of the C2, C3, C4, C5, C6, and C7 vertebra,
respectively (Fig. 4G). Furthermore, a classification with positive on the kyphosis and negative on lordosis
to meet the needs of different research communities.

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Fig. 4 Schematic diagram of quantitative parameters.

7. Cervical curvature: C2-7 Cobb angle is measured from the inferior endplate of C2 to the inferior endplate
of C7, C2-6 Cobb is measured from the inferior endplate of C2 to the inferior endplate of C6, and C2-7
SVA is centroid of C2 and the posterior superior aspect of C725 (Fig. 4F). Toyama Curvature19: the AB
line (in Fig. 4I) refers to the line connecting the midpoint of the lower endplate of the C2 vertebra to the
midpoint of the upper endplate of the C7 vertebra. Based on the position and distance of the centroids
relative to the AB line, the cervical spine can be categorized into the following groups: Lordotic group:
All centroids are anterior to the AB line, and the distance between at least one centroid and the AB line is
2 mm or more; Straight group: The distance between the AB line and each centroid is less than 2 mm; Sig-
moid group: Some centroids are anterior and some are posterior to the AB line, and the distance between
the AB line and at least one centroid is 2 mm or more; Kyphotic group: All centroids are posterior to the AB
line, and the distance between at least one centroid and the AB line is 2 mm or more. We further classified
the posterior convexity of the C3 and C4 vertebral body as Sigmoid 1, and the posterior convexity of the C5
and C6 vertebral body as Sigmoid 2. The distance between the AB line and at least one centroid is 2 mm or
more (Fig. 4I). Cervical Curvature Index26 (CCI) measures cervical curvature by determining the distance
from the posteroinferior edge of the C3-C6 vertebral bodies to a straight line drawn from the posteroinfe-
rior edge of C2-C7 [CI = (A + B + C + D)/E × 100], A: Distance from the posteroinferior edge of C3 to the
line, B: Distance from the posteroinferior edge of C4 to the line, C: Distance from the posteroinferior edge
of C5 to the line, D: Distance from the posteroinferior edge of C6 to the line, E: Total distance from the
posteroinferior edge of C2-C7 to the line (Fig. 4E). The Centroid Measurement of Cervical Lordosis (CCL)
method19 refers to the angle formed between the line connecting the midpoint of the lower endplate of C2
to the centroid of C3, and the line connecting the centroids of C6 and C7. In previous study, this value was
considered negative when the C2-C3 line was posterior to the C6-C7 line. However, this negative value
actually represents a normal physiological curvature. Therefore, for consistency in the study of cervical
lordosis, we have redefined the situation where the C2-C3 line is posterior to the C6-C7 line as a positive
value (Fig. 4E,F,I).
8. Vertebral Angle26: The vertebral body angle is the angle between the upper and lower endplates, and a
classification with positive on the posterior side of the vertebral body and negative on the anterior side was
provided (Fig. 4H).

Algorithm. The objective of image keypoints annotation is to derive quantitative parameters for medical diag-
nostics and treatment. We have devised an advanced algorithm that transforms 23 image keypoints into 77
detailed quantitative parameters. This algorithm effectively combines all previously described calculation meth-
ods and formulas, facilitating an automated, efficient, and accurate keypoints-based computation. The algorithm
initiates with the establishment of a ‘points_dict’, a foundational step in correlating key points within images
to their respective numerical indices. It employs ‘cal_dist_adj_row’ and ‘cal_dis_adj_col’ for the precise cal-
culation of distances between proximate points, whether arrayed in rows or columns. In the realm of angular

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Age Lordotic Straight Sigmoid1 Sigmoid2 Kyphotic Total

18–20 (age) 9 10 4 4 6 33
20–30 (age) 401 496 65 214 190 1366
30–40 (age) 617 625 110 217 204 1773
40–50 (age) 298 296 40 131 66 831
50–60 (age) 222 169 49 56 19 515
60–70 (age) 166 100 35 35 15 351
70–80 (age) 46 12 12 5 2 77
80–90 (age) 6 4 3 2 2 17
Total 1765 1712 318 664 504 4963

Table 1. Age distribution of cervical spine curvature (Modified Toyama).

Calculation of Pixel equivalent

y = Pixel equivalent

a = Pixel distance a

b = Real world distance

b

Fig. 5 Schematic diagram of the calculation process for pixel equivalent.

measurements, the algorithm utilizes ‘cal_angle’, ‘cal_angle_adj’, and ‘cal_angle_not_adj’. Here, ‘cal_angle’ is
responsible for computing the angular relationship in a quartet of points, while ‘cal_angle_adj’ and ‘cal_angle_
not_adj’ systematically calculate angles between adjacent and non-adjacent points, respectively. Additionally, the
algorithm encompasses functions such as ‘cal_sva’, ‘cal_c_type’, ‘cal_cns’, ‘cal_cn’, and ‘cal_toyama’ for the quanti-
fication of critical spinal parameters, including the sva and cobb angles. Integral to this framework are advanced
auxiliary functions like ‘cal_intersection_points’, ‘point_position_relative_to_line’, and ‘cal_dist_point_line’,
which are instrumental in executing sophisticated geometric computations. The final step of the algorithm
employs the ‘cal_json_folder’ function, which methodically reads each JSON file, performs the necessary cal-
culations, and compiles the results into an Excel file, thereby completing the synthesis of a comprehensive set
of cervical spine metrics. The final output of the algorithm, consisting of 77 quantified parameters, is manually
categorized to yield 118 ultimate results to meet the diverse requirements for the parameters.

Population distribution. The CSXA encompasses a total of 4963 individuals, consisting of 3202 females and
1761 males. The age distribution across the entire cohort ranged from 18 to 87 years, with a majority, aged
between 20 and 70 years accounting for 4824 individuals. There are 4782 symptomatic patients with cervical
pain or cervical spondylosis symptoms and 181 asymptomatic individuals. A detailed distribution of age and
curvature can be found in Table 1.

Pixel equivalent. Every raw image comes with a linear scale featuring distinct graduated markings of varying
lengths and intervals, which allows us to convert the pixel distance between two pixels into the real-world dis-
tance by drawing a line along the scale of the image17. These graduated markings are meticulously recorded in
an Excel spreadsheet for reference. Subsequently, a Python script is developed to uniformly compute the pixel
distances of each scale within the images. Ultimately, the pixel equivalent is accurately calculated by dividing the
pixel values of the scale in each image by the corresponding graduated markings (Fig. 5).

Data Records
All demographic categorizations, spinal curvature data, gender, age, and pixel equivalent information have been
recorded in the Excel file named “dataset”. This document, along with the code, is available on GitHub at https://
github.com/yran888/CSXA-dataset.git. The entire image dataset has been stored in the ‘datasets’ folder, which
includes two subfolders: ‘datasets-PNG’ and ‘datasets-JSON’. The folder has been uploaded to Science Data
Bank27 and can be accessed at https://doi.org/10.57760/sciencedb.15391.

Technical Validation
Keypoints annotation validation. The annotations of the image underwent three meticulous cross-check-
ing. Additionally, a Python script was developed to examine the count and nomenclature of all annotation points.

Pixel value validation. Random sampling measurements were conducted using ImageJ (https://imagej.net/
ij/download.html) to validate the consistency of results computed by python code.

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Quantitative parameter validation. Random cervical spine X-rays were sampled and measured using
the PACS system for all quantitative parameters to verify the consistency between algorithm measurements and
manual measurements.
Results. The annotations for all keypoints positions, counts, and names were accurate, and the algorithm
measurements aligned consistently with the manual measurements.
Code availability
The Python code used in this paper was developed in version 3.11.0 and is available for free access. The first
code, ‘pixel equivalent’, is designed to calculate the pixel values of linear scales in images. The second code, which
consists of ‘aux_info_cal’ and ‘test’, is used to calculate quantitative parameters.

Received: 23 January 2024; Accepted: 15 May 2024;

Published: xx xx xxxx

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Acknowledgements
We would like to express our sincere gratitude to the doctors, students, and colleagues who have actively
participated in this project over the past two years. Their dedication and support have been invaluable in the
successful completion of this work. This project has been funded in part with Ministry of Education in China,
Contract No. 90020371420002.

Author contributions
Yu Ran, Wanli Qin and Changlong Qin are co-first authors. Yu Ran completed the writing, Changlong Qin
completed the acquisition and coding of the original pictures, Wanli Qin and Changlong Qin jointly completed
the initial annotation of the images, and Yu Ran further modified all the annotated images. Jiang Chen conducted
the final review of the annotation points. The code was developed by Yu Ran and Xiaobin Li, while Yuxiang Dai
provided technical support. Dongran Han designed the overall framework of the article, Yixing Liu and Bei Wang
completed the proofreading. Li Yan helped with the grammatical revision and language polishing. Xiaohong Mu
and Lin Xu made important contributions in the original data extraction and paper review.

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Competing interests
These authors declare no competing interests.

Additional information
Correspondence and requests for materials should be addressed to J.C. or D.H.
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