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Bronchopulmonary segments approximation using anatomical atlas

Article  in  Proceedings of SPIE - The International Society for Optical Engineering · March 2007
DOI: 10.1117/12.709651

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 Bronchopulmonary Segments Approximation using Anatomical Atlas
Sata Busayarata and Tatjana Zrimecab
a
School of Computer Science and Engineering, University of New South Wales, Australia
b
Centre for Health Informatics, University of New South Wales, Australia

ABSTRACT

Bronchopulmonary segments are valuable as they give more accurate localization than lung lobes. Traditionally,
determining the segments requires segmentation and identification of segmental bronchi, which, in turn, require
volumetric imaging data. In this paper, we present a method for approximating the bronchopulmonary segments for
sparse data by effectively using an anatomical atlas. The atlas is constructed from a volumetric data and contains
accurate information about bronchopulmonary segments. A new ray-tracing based image registration is developed for
transferring the information from the atlas to a query image. Results show that the method is able to approximate the
segments using sparse HRCT data with slice gap up to 25 millimeters.
Keywords: Bronchopulmonary segments, lung, HRCT, atlas, registration

1. INTRODUCTION
Image localization is one of the important processes for medical image analysis. Radiologists frequently use localization
to help distinguish between similar disease patterns. The information also helps them to determine the distribution of the
patterns, which facilitate diagnosis and treatment. In lung images, localization is relatively difficult because of the lack of
visible landmarks inside the lungs. Modern imaging modalities, such as High-resolution CT (HRCT), make a more
accurate localization possible since many small lung structures like fissures, secondary lobules and sub-segmental
bronchi are visible. However, a HRCT scan contains a large number of images so it is impractical for a radiologist to
manfully perform accurate localization. An automated lung localization method is then required.
Several automated lung localization methods have been reported. Most of them utilize the visible pulmonary fissures to
divide lungs into lobes [1, 2]. Unfortunately, it has been reported that, for a noticeably amount of cases, fissures are
widened, incomplete or even absent, making robust fissure detection difficult. Zrimec et al. [3] uses landmark that are
outside the lung, such as bones, to divide lungs into clinically meaningful regions. The method is robust since the
landmarks are stable and relatively easy to detect. Although the regions provide useful information, in some cases, more
detailed information about the lung structure is required. Krass et al. [4] and Hiroko et al. [5] divide lung into
bronchopulmonary segments, which is a further division of the lobes. Different segments are defined by the segmental
bronchi that supply them. Bronchopulmonary segments provide more localized information but their determination
requires bronchial tree segmentation, which can be unreliable in a present of some diseases.
In this paper, we propose a robust method for automatic bronchopulmonary segments approximation. We recognize the
clinical value of the segments as they are the smallest subdivisions of the lung that have a relatively constant spatial
arrangement [6]. We also recognize the advantages of being able to apply our method to a sparse HRCT scan (has gaps
between slices). Even though volumetric HRCT is fast becoming the standard in the advent of the multi-slice scanner,
the sparse HRCT is still used in many clinical situations, for example, when the radiation dose to the patient is
concerned. Sparse HRCT also requires significantly smaller storage and less time to process, by radiologists or
computers. Determining bronchopulmonary segments using the method in [4] cannot be applied to the sparse data, given
big enough slice gaps, because accurate bronchial tree segmentation requires volumetric data with no slice gaps. Our
method determines the segments by registering a patient lung to a lung atlas that contains the bronchopulmonary
segments information. In section 2 and 3, lung atlas construction and our new atlas-to-image registration will be
discussed. In section 4, an application of bronchopulmonary segments approximation will be illustrated. Lastly, results
will be presented and discussed.
 2. THE ATLAS
The three-dimensional lung atlas used for this work is created from a volumetric HRCT scan of relatively normal lungs.
It contains information about various anatomical landmarks. Lung surfaces are automatically detected using adaptive
thresholding and active contour snakes in 2D developed by [7]. We modified the method so that it takes the third-
dimension continuity into account. Single-point landmarks, namely carina, sternum, spinal cord and lung roots, are
manually identified to ensure the correctness. The lung surface model and the landmarks are shown in Fig. 1 – top row.

Fig. 1. Lung atlas with landmarks and pulmonary segments

Information about the pulmonary segments is included in the atlas (See Fig. 1. – bottom row). To model the segments, a
complete bronchial tree is needed. Two-dimensional seeded region growing with leaking prevention and three-dimension
tree tracing, similar to [8], are used to automatically segment the bronchial tree. The seed point is also automatically
determined by detecting the trachea in the first image in the scan (circular black object near the middle of the body). Our
algorithm has an ability to continue the trace even though the region growing fails to detect a bronchus on one image by
skipping to the next images. This improvement is significant because, in our dataset, many bronchi have poor
appearances on one 2D image due to volume averaging or imaging artifacts but their appearances improve on the next
image.
Even with the improvement, the automatic bronchial tree detection algorithm does not achieve the same accuracy as the
lung surface detection. The sensitivity of the detection algorithm drops after it reaches the 4th generation of bronchi. This
is because the bronchi of this type are less than two millimeters (about four pixels) in diameters. With such small size,
the effect of the volume averaging is much greater. It often increases the intensity of the entire lumen and, thus, fails the
region growing threshold test. In order to construct an accurate model of the bronchial tree, some human intervention is
needed. An interactive tool was developed. It allows an expert user to manually mark a 2D bronchus that the algorithm
missed and then ask the algorithm to continue the trace from there. It also allows a user to remove false positives
produced by the algorithm. Fig 2. shows an example of bronchial tree before and after manual intervention.
The same tool also allows user to divide the whole bronchi tree into different segmental branches with minimum effort.
The branches are used to divide the lung parenchyma into lung segments. Multiple-seed-three-dimensional region
growing is used for the division. For each of the segmental branches, its region grows to the neighboring voxels. All
regions grow simultaneously and stop when reaching the lung surface or other regions (See Fig. 3). Each fully grown
region will represent a bronchopulmonary segment.

Fig. 2. Automatically detected 3D bronchial tree (left) and with manual extensions in red color (right)

Fig. 3. Step-to-step volume growing of bronchopulmonary segments

3. LUNG REGISTRATION
To apply the knowledge encoded in the atlas to an image of another scan, an atlas-to-image registration is developed.
Similar to how radiologists map an image to a pictorial atlas, our registration is based on anatomical landmarks and
interpolation. Lung root is used to initially align a query scan to the atlas. The lung surface of the query scan is then
deformed to match the atlas’s surface. The correspondences of voxels inside the lung are determined by thee-
dimensional interpolation. The deformation and interpolation are achieved by 3D ray tracing.
Ray tracing is a technique usually used in the field of computer graphics for finding correspondence between pixels on
the screen and points on the scene for real-time and offline rendering. - In our case - we use ray tracing to find
correspondences between voxels in a query scan and the lung atlas.
We use Fig. 4. to demonstrate how the method works, we are given a lung surface of a query sparse scan (S) and another
lung surface of the lung atlas (A) and we want to register point P in S to A. (In another word, to find the corresponding
point of P in A). We trace a 3D ray from the lung root (O), through the point P, until it hits both lung surfaces (S and A).
The surface hitting points are called PS and PA respectively. The registered point (R) is calculated given O, P, PS and PA
as shown in Eq. 1. A P-R pair is called a voxel correspondence between query scan and the atlas.
R = O + (|OP| × |OPA| / |OPS|) (1)
For the sparse scan, a complete lung surface needs to be approximated because a ray may hit the surface in between slice
gap. The surface approximating algorithm works as follows. A number of triangle strips are generated by connecting
lung boundary points between two consecutive slices. Scan-line triangle filling algorithm [11] is then used to fill the
triangle strips. The scan-line algorithm is commonly used in computer graphics and is thus implemented in most of the
VGA cards, which our surface approximation can benefit from. An example is shown in Fig. 5.

Fig. 4. Ray-tracing based lung registration. S is the query lung surface, A is the atlas surface, O is the common lung root, P
is the query point, PS and PA is the surface hitting points of S and A, respectively and R is the registered point.

Fig. 5. Sparse lung surface (left) and its complete surface resulted from our surface approximation algorithm (right)
 4. BRONCHOPULMONARY SEGMENTS APPROXIMATION
Anatomically, adjacent bronchopulmonary segments are physically separated by connective tissue septa [6].
Unfortunately, the septa are not recognizable on HRCT. Generally, the segments are determined by distance from
segmental bronchi. Segmenting bronchial tree and labeling its segmental bronchi require volumetric data, even by
manual operations. This makes the determination of the segments on sparse data virtually impossible. However, with the
lung atlas that contains accurate bronchopulmonary segments information and the atlas-to-image registration, it is
possible to approximate the segments on sparse data.
The registration technique described in section 3 is used to find correspondences (R-P couples, see Fig. 4) for every in-
lung voxel in the sparse scan. R is a voxel in the atlas and is priory assigned to one of the segments. We then assign the
corresponding voxel in the sparse scan, P, to the same segment as in the atlas. A 2D example of the registered regions on
an HRCT slice is shown in Fig. 6.
An optimization for registering a large number of voxles is also implemented. It exploits the fact that, when registering
an entire lung, one 3D ray usually passes more than one query voxel. In another word, more than one voxel uses the
same 3D ray to be registered. Since the ray tracing and finding the surface hitting points (PS, PA) are expensive
processes, the surface hitting points are cached to be reused for other voxels lying on the same 3D direction. The cache is
implemented using a hash table with the hash function calculated from a normalized vector of OP. Both algorithmic
analysis and an experiment have shown that that the caching reduces the computation by about three times.

LIPo
RIPo

LISu
RILa
LILa
RISu
RIAn LIAn
LSIn
RMMe
RMLa LSSu

RSAn
LSAn
RMMe

Fig. 6. Approximated bronchopulmonary segments

5. RESULT
To evaluate how accurate the registered regions are, we need a reference standard of such regions to compare with. A
conventional way of using radiologist-labeled regions would not work for this particular application because the
boundaries of bronchopulmonary segments are not visible on HRCT. To overcome the limitation, we constructed two 3D
atlases of the bronchopulmonary segments using the procedure described in section 2 and had the labeled segmental
branches verified by an experience radiologist before performing segment volume growing. One of the two atlases was
used as the reference standard and the other one was used as the atlas for registration. The process was repeated with the
two atlases switching roles. This evaluation method also allowed us to compare the performance at different sparseness
i.e. the gaps between slices. A visual comparison of the result and its reference standard is shown in Fig. 7 and the
performance measures are shown in Table 1. The performance measures include the accuracy, which is the direct
comparison against the reference standard, and the average distance from correct class, which provides more details on how
much incorrect the result is.
The result in Table 1 indicates relatively low accuracy. However, the low average distance from the correct class and
the visual result show that the method provides good approximation of the bronchopulmonary segments. The result also
demonstrates that the ray-tracing registration is capable to work with sparse data with slice gaps as great as 25mm. In
fact, compared with 5mm data, using 25mm-gap data only decreases the accuracy by 6% and increase the average
distance from the correct class by 0.3 millimeters.
We also evaluate the method with larger number of patient scans to ensure the robustness of the method. HRCT scans
from 38 patients were used for this evaluation. The images were acquired as a part of normal clinical practice using
standard imaging protocols. The images were taken using a SIEMENS scanner, with 512x512 spatial resolution, 1.0mm
slice thickness and 15mm slice gap (~20 images per study). The data are stored in Dicom format as 16-bit grayscale
images, with the pixel intensity proportional to tissue density.
The second evaluation procedure went as follows. We applied the bronchopulmonary segments approximation method
on the test data. Unfortunately, unlike the first evaluation, the reference standard for this data was not available. We
performed an approximated evaluation by using segment-to-lung proportions (SLP) describe in Eq. 2. The evaluation is
based on the knowledge that the segment-to-lung proportions of any lungs should be approximately invariable. The
results in Table 2 show that the approximated segments and the verified segmented from the atlas have similar SLP. The
average differences are 10% and 22% for right and left lung, respectively. The reasonably low standard deviations
(24.5%) show that the SLP are also similar among the test set.
SLP(s_id) = |S(s_id)| / |L| (2)
S(s_id) = {v є I | v.s_id = s_id}
L = {v є I | inLung(v) = TRUE}
where, I is Image space
inLung(v) tests if v is inside the lung

Fig. 7. Result from our lung segment approximation on 15mm-gap data (left) and the reference standard used for comparison (right)
Table 1. Performance of the bronchopulmonary segments approximation measured in accuracy and average distance from
the correct class at different slice gaps.
Accuracy Average distance
Slice gap from correct class
Fold1 Fold2 Average
5mm 55.8% 58.9% 57.4% 3.2mm
15mm 52.1% 54.0% 53.1% 3.5mm
25mm 50.9% 51.8% 51.4% 3.5mm

Table 2. Comparison between segment-to-lung proportions (SLP) of the test data and the atlas
Test Atlas Test Atlas
Segment Diff Segment Diff
SLP±sd% SLP% SLP±sd% SLP%
RSAp 14.8±4.0 17.2 2.4 LSAp 7.0±2.2 8.1 1.1
RSPo 9.3±2.4 8.7 0.6 LSPo 17.7±3.6 17.0 0.7
RSAn 11.3±1.9 11.1 0.2 LSAn 7.4±1.6 12.9 5.5
RMLa 5.9±1.4 5.9 0.0 LSSu 11.0±2.2 14.6 3.6
RMMe 12.7±3.7 15.0 2.3 LSin 6.0±2.9 7.2 1.2
RISu 11.4±3.2 10.1 1.3 LISu 13.4±2.4 11.3 2.1
RIAn 11.2±3.1 11.3 0.1 LIAn 4.1±1.3 3.0 1.2
RIMe 4.3±0.8 2.76 1.5 LIMe 14.3±3.1 10.5 3.8
RILa 6.2±1.2 6.53 0.3 LILa 4.7±1.2 3.1 1.6
RIPo 12.8±3.6 11.28 1.5 LIPo 14.2±4.0 12.2 2.0
Average 10.0±2.5 10.0 1.0 Average 10.0±2.4 10.0 2.2

6. DISCUSSION AND CONCLUSIONS

We have presented a new method for bronchopulmonary segments approximation on HRCT. The method employed a
novel ray-tracing-based lung registration to transfer bronchopulmonary segments information from the lung atlas to a
query scan.
Using two bronchopulmonary-segment models, which were validated by a radiologist, we evaluate the method by
comparing the registered bronchopulmonary segments against each other at different level of sparseness. While the
registered segments are not directly matched with the reference standard (53.1% accuracy for data with 15mm gaps), the
distance between them are small (3.5mm). The result also shows that the method is able to approximate the pulmonary
segments using sparse HRCT data. Compared with the previous approaches that require volumetric data with no slice
gaps and rely on not-yet-reliable bronchial tree segmentation, the results emphasize the effectiveness of using
deformable atlases for medical image analysis. With the high robustness indicated by the second evaluation, this for
bronchopulmonary segments approximation application has high potential for being used in real clinical environment to
help radiologists in detailed lung localization.

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