Method and system for performing multi-bone segmentation in imaging data

• US 9,801,601 B2
• Filed: 12/29/2015
• Issued: 10/31/2017
• Est. Priority Date: 12/29/2015
• Status: Active Grant

• Current Assignee: Laboratoires Bodycad Inc
• Original Assignee: Laboratoires Bodycad Inc
• Inventors: Rivet-Sabourin, Geoffroy, Randrianarisoa, Vnre Rakotomalala
• Primary Examiner(s): AZARIAN, SEYED H
• Application Number:
  US14/982,029
• Publication Number:
  US 20160275674A1
• Time in Patent Office: 672 Days
• Field of Search: 382100, 382103, 382106-107, 382128-132, 382154, 382162, 382168, 382173, 382181, 382199, 382232, 382254, 382266, 382274, 382276, 382285-291, 382305, 382312, 324309, 324300, 378 4, 378 16, 378 21
• CPC Class Codes: A61B 5/055 involving electronic [EMR] or nuclear [NMR] magnetic resonance, e.g. magnetic resonance imaging
• CPC Class Codes: A61B 5/4504 Bones A61B5/4547 takes precedence
• CPC Class Codes: A61B 5/4528 Joints A61B5/4533, A61B5/4538 take precedence
• CPC Class Codes: A61B 6/032 Transmission computed tomography [CT]
• CPC Class Codes: A61B 6/505 for diagnosis of bone
• CPC Class Codes: A61B 6/5211 involving processing of medical diagnostic data
• CPC Class Codes: G06T 2207/10072 Tomographic images
• CPC Class Codes: G06T 2207/20036 Morphological image processing
• CPC Class Codes: G06T 2207/20161 Level set
• CPC Class Codes: G06T 2207/30008 Bone
• CPC Class Codes: G06T 7/11 Region-based segmentation
• CPC Class Codes: G06T 7/12 Edge-based segmentation
• CPC Class Codes: G06T 7/136 involving thresholding
• CPC Class Codes: G06T 7/174 involving the use of two or more images

Abstract

A computer implemented method for performing bone segmentation in imaging data of a section of a body structure is provided. The method includes: Obtaining the imaging data including a plurality of 2D images of the section of the body structure; and performing a multiphase local-based hybrid level set segmentation on at least a subset of the plurality of 2D images by minimizing an energy functional including a local-based edge term and a local-based region term computed locally inside a local neighborhood centered at each pixel of each one of the 2D images on which the multiphase local-based hybrid level set segmentation is performed, the local neighborhood being defined by a Gaussian kernel whose size is determined by a scale parameter (σ).

Claims

1. A computer implemented method for performing bone segmentation in imaging data of a section of a body structure, the method comprising:

Using a processor,

Obtaining the imaging data including a plurality of 2D images of the section of the body structure; and

Performing a multiphase local-based hybrid level set segmentation on at least a subset of the plurality of 2D images by minimizing an energy functional including a local-based edge term and a local-based region term computed locally inside a local neighborhood centered at each pixel of each one of the 2D images on which the multiphase local-based hybrid level set segmentation is performed, the local neighborhood being defined by a Gaussian kernel whose size is determined by a scale parameter (σ

);

Generating a 3D volume including a plurality of 3D subvolumes from the segmented blobs of the secondary segmented image data; and

Associating an anatomical component to each one of the 3D subvolumes using the anatomical knowledge data relative to the

section of the body structure of the imaging data.

2. The computer implemented method of claim 1, wherein the local neighborhood is circular and performing the multiphase local-based hybrid level set segmentation further comprises:

for each pixel of the 2D images, dynamically changing region descriptors based on a position of a center of the local neighborhood.

3. The computer implemented method of claim 1, further comprising:

selecting a value of λ

to adjust a performance of the multiphase local-based hybrid level set segmentation with λ

being greater than 0 and smaller than 1, wherein λ

multiplies the local-based edge term and (1−

λ

) multiplies local-based region term.

4. The computer implemented method of of claim 1, wherein the 2D images include two phases and the energy functional is:

_2-phase(φ

,c,b)=(1−

λ

)_region(φ

,c,b)+λ

_edge(φ

)+μ

_p(φ

)

where λ

is greater than or equal to 0 and smaller than or equal to 1, μ

is a positive constant, b is a bias field accounting for intensity inhomogeneity, and c is a vector representing intensity-based constant values in disjoint regions,

_edge(φ

)=ν

_g(φ

)+α

_g(φ

)

wherein ν and

α

are normalization constants,

5. The computer implemented method of of claim 1, wherein the energy functional is:

_multiphase(Φ

,c,b)=(1−

λ

)_region(Φ

,c,b)+λ

_edge(Φ

)+μ

_p(Φ

)

where λ

is greater than or equal to 0 and smaller than or equal to 1, μ

is a positive constant, b is a bias field accounting for intensity inhomogeneity, c is a vector representing intensity-based constant values in disjoint regions, and φ

is a vector formed by k level set functions φ

i, i=1 . . . k for k regions or phases;

Φ

=(φ

₁(y), . . . ,φ

_k(y))

and a number of the level set functions to be used is at least equal to;

k=log₂()

where log₂ is the logarithm to the base 2 and N is the number of the regions to be segmented in the image.

_region(Φ

,c,b)=∫

Σ

_i=1^Ne_i(x)M_i(Φ

)x))dx

With;

e_j(x)=∫

K_σ

|I(x)−

b(y)c_i|²dy, i=1, . . . ,k

with K_σ

, a kernel function computed by means of a truncated Gaussian function of standard deviation σ

, referred to as the scale parameter,

_i is a membership function of each region Ω

_i, and is defined as;

6. A computer implemented method for performing bone segmentation in imaging data of at least a section of a body structure including a plurality of bones using anatomical knowledge data relative to the section of the body structure of the imaging data, the method comprising:

Obtaining the imaging data including a plurality of 2D images of the section of the body structure;

Generating primary image data from the imaging data using an image preprocessing including identifying regions of interest (ROIs) in the 2D images;

Generating secondary segmented image data including a plurality of 2D binary images with segmented blobs by performing a multiphase local-based hybrid level set segmentation on the regions of interest (ROIs) by minimizing an energy functional including a local-based edge term and a local-based region term computed locally inside a local neighborhood centered at each point of a respective one of the regions of interest (ROIs), the local neighborhood being defined by a Gaussian kernel;

Generating a 3D volume including a plurality of 3D subvolumes from the segmented blobs of the secondary segmented image data; and

Associating an anatomical component to each one of the 3D subvolumes using the anatomical knowledge data relative to the section of the body structure of the imaging data.

7. The computer implemented method of claim 6, wherein the plurality of 2D images are greyscale images and the image preprocessing further comprises performing a 3D adaptive thresholding processing to define thresholded blobs in the 2D images and generating binary masks from the thresholded blobs obtained by the 3D adaptive thresholding processing, wherein the 3D adaptive thresholding processing includes the steps of:

For at least a sample of the plurality of 2D greyscale images;

Dividing each one of the 2D greyscale images of at least the sample in a plurality of sections;

Computing a local pixel intensity section threshold for each one of the sections;

Computing a global image pixel intensity threshold for each one of the 2D greyscale images of at least the sample using the local pixel intensity section thresholds computed for each one of the sections;

Computing a global volume pixel intensity threshold using the global image pixel intensity thresholds; and

Applying the global volume pixel intensity threshold to each one of the 2D greyscale images of the plurality of 2D greyscale images.

8. The computer implemented method of claim 7, wherein the global image pixel intensity threshold for each one of the 2D greyscale images of at least the sample is computed as a maximum of the local pixel intensity section thresholds for the corresponding image;

and the global volume pixel intensity threshold from the global image pixel intensity thresholds is computed as a mean of the global image pixel intensity thresholds minus 1.5 times a standard deviation of the global image pixel intensity thresholds [mean(global image pixel intensity thresholds)−

1.5std(global image pixel intensity thresholds)].

9. The computer implemented method of claim 7, wherein the image preprocessing comprises computing thresholded blobs in the images following the 3D adaptive thresholding processing and creating binary masks from the thresholded blobs;

and wherein identifying regions of interest (ROIs) in the 2D images comprises selecting regions in the 2D greyscale images of the imaging data including at least one of the a respective one of the thresholded blobs and a respective one of the binary masks generated from the thresholded blobs.

10. The computer implemented method of claim 9, wherein generating secondary segmented image data comprises performing a blob masking validation following the multiphase local-based hybrid level set segmentation, the multiphase local-based hybrid level set segmentation generating a plurality of unmasked blobs, and wherein the blob masking validation comprises:

Applying the binary masks to the unmasked blobs to obtain masked blobs;

Determining at least one perceptual grouping property of each one of the masked blobs and the unmasked blobs;

For each corresponding pair of masked blobs and unmasked blobs,

Comparing the at least one perceptual grouping property of the masked blob to the at least one perceptual grouping property of the corresponding one of unmasked blobs; and

Selecting the one of the masked blob and the corresponding one of unmasked blobs having the highest perceptual grouping property as the segmented blob of the secondary segmented image data.

11. The computer implemented method of claim 9, further comprising initializing the multiphase local-based hybrid level set segmentation with the binary masks.

12. The computer implemented method of claim 9, wherein performing the multiphase local-based hybrid level set segmentation on the regions of interest (ROIs) comprises generating binary subimages including the segmented blobs and the method further comprises merging the binary subimages to generate a respective one of the 2D binary images including the segmented blobs.

13. The computer implemented method of claim 6, wherein the image preprocessing further comprises:

Determining an initial image including at least one region of interest and determining a final image including at least one region of interest; and

Selecting a subset of 2D images including the initial image, the final image, and the images extending therebetween, wherein the primary image data consists of the subset of 2D images including the regions of interest (ROIs).

14. The computer implemented method of claim 6, wherein identifying anatomical components in the 3D volume comprises:

Computing at least one subvolume feature for each one of the 3D subvolumes;

For each one of the 3D subvolumes, carrying out a bone identification processing comprising;

Identifying a closest one of the bones and comparing the at least one subvolume feature to features of the anatomical knowledge data corresponding to the closest one of the bones;

If the at least one subvolume feature for the respective one of the 3D subvolumes substantially corresponds to the features of the anatomical knowledge data for the closest one of the bones, associating the respective one of the 3D subvolumes to the closest one of the bones;

Otherwise, applying a selective 3D bone separation to the respective one of the 3D subvolumes and generating new 3D subvolumes.

15. The computer implemented method of claim 14, wherein identifying anatomical components in the 3D volume further comprises:

Identifying a 3D anatomical point of interest within the 3D volume;

Identifying a 3D subvolume closest to the 3D anatomical point of interest; and

Performing sequentially the bone identification processing by proximity to a last one of associated 3D subvolumes, starting from the 3D subvolume closest to the 3D anatomical point of interest.

16. The computer implemented method of claim 14, wherein the 3D volume generated from the 2D binary images of the secondary segmented image data is a first 3D volume and the method further comprises:

Carrying out a 2D blob separation on the secondary segmented image data and generating a second 3D volume by stacking binary images obtained following the 2D blob separation; and

wherein identifying anatomical components is performed on the second 3D volume.

17. The computer implemented method of claim 16, wherein carrying out a 2D blob separation comprises:

For each one of the segmented blobs of the secondary segmented image data;

Creating straight segments from the contours of the respective one of the segmented blobs;

Identifying points of interest using the straight segments;

If there is at least one point of interest, identifying at least one bone attachment location close to the at least one point of interest; and

separating the respective one of the segmented blobs by local morphological erosion along the at least one bone attachment location.

18. The computer implemented method of claim 17, wherein identifying points of interest using the straight segments comprises:

Determining a length of the straight segments and an angle between consecutive ones of the straight segments, the consecutive one of the straight segments sharing a common point;

For each pair of consecutive straight segments (s₁, s₂), computing a relevance measure (K_relevance);

19. The computer implemented method of claim 18, wherein identifying at least one bone attachment location close to the at least one point of interest comprises:

Identifying if a respective one of the points of interest belongs to a linear bone attachment location defined by a pair of points of interest; and

, for each identified linear bone attachment location, separating the respective one of the segmented blobs comprises performing a linear local morphological erosion along a line extending between the points of interest defining the linear bone attachment location;

otherwise, identifying the respective one of the points of interest as a punctual bone attachment location and separating the respective one of the segmented blobs comprises performing local morphological erosion around the punctual bone attachment location.

20. The computer implemented method of claim 19, wherein identifying a pair of points of interest comprises:

for each potential pair of points of interest, grouping the points of interest in a pair and computing a distance separating two grouped points of the pair, comparing the computed distance to a predetermined distance threshold; and

if the computed distance meets the predetermined distance threshold, associating the potential pair of interest points as being one linear bone attachment location.

21. The computer implemented method of claim 6, wherein the local neighborhood is circular and performing the multiphase local-based hybrid level set segmentation further comprises:

for each pixel of the regions of interest (ROIs), dynamically changing region descriptors based on a position of a center of the local neighborhood.

22. The computer implemented method of claim 6, further comprising:

selecting a value λ

of to adjust the performance of the multiphase local-based hybrid level set segmentation with λ

being greater than 0 and smaller than 1, wherein λ

multiplies the local-based edge term and (1−

λ

) multiplies local-based region term.

23. A system for generating segmentation data segmentation from imaging data of at least a section of a body structure including a plurality of bones using anatomical knowledge data relative to the section of the body structure of the imaging data, the system comprising:

a processing unit having a processor and a memory;

an image preprocessing module stored on the memory and executable by the processor, the image preprocessing module having program code that when executed, generates primary image data from the imaging data using an image preprocessing process, the primary image data including regions of interest in images of the imaging data;

a multi-bone segmentation module stored on the memory and executable by the processor, the multi-bone segmentation module having a program code that when executed, generates a 3D volume by performing a multiphase local-based hybrid level set segmentation to obtain a plurality of segmented blobs and combining the segmented blobs to obtain the 3D volume including a plurality of 3D subvolumes, the multiphase local-based hybrid level set segmentation being carried out on each one of on the regions of interest (ROIs) by minimizing an energy functional including a local-based edge term and a local-based region term computed locally inside a local neighborhood centered at each point of a respective one of the regions of interest (ROIs), the local neighborhood being defined by a Gaussian kernel and generating a 3D volume following the multiphase local-based hybrid level set segmentation; and

an anatomical component identification module stored on the memory and executable by the processor, the anatomical component identification module having a program code that, when executed, generates tertiary segmented imaging data through identification of the subvolumes defined in the 3D volume and identification of bones defined by the subvolumes.