Automatic method and system for vessel refine segmentation in biomedical images using tree structure based deep learning model

1. A system for segmenting a biomedical image including at least one tree structure object, comprising:

a communication interface configured to receive the biomedical image and a learning model, the biomedical image being acquired by an image acquisition device; and

at least one processor, configured to:

extract a plurality of image patches from the biomedical image; and

apply the learning model to the plurality of image patches to segment the biomedical image, wherein the learning model includes a convolutional network configured to process the plurality of image patches to construct respective feature maps and a tree structure network configured to process the feature maps collectively to obtain a segmentation mask for the tree structure object, wherein the tree structure network models a spatial constraint of the plurality of image patches.

2. The system of claim 1 , wherein to extract the plurality of image patches, the at least one processor is further configured to:

determine a centerline of the tree structure object in the biomedical image; and

extract the plurality of image patches along the centerline.

3. The system of claim 1 , wherein the convolutional network includes a plurality of fully convolutional networks each configured to process an image patch.

4. The system of claim 3 , wherein the plurality of fully convolutional networks process the plurality of image patches in parallel.

5. The system of claim 1 , wherein the tree structure network is a tree structure convolution recurrent neural network.

6. The system of claim 1 , wherein the spatial constraint is determined based on a tree structure of the image patches.

7. The system of claim 1 , wherein the spatial constraint is determined based on a spatial relationship between two neighboring image patches among the plurality of image patches.

8. The system of claim 1 , wherein the convolutional network and the tree structure network are trained jointly using a gradient descent based method.

9. The system of claim 1 , wherein the tree structure object is a blood vessel.

10. The system of claim 1 , wherein the biomedical image is a 3D image including a plurality of 2D image slices, wherein the plurality of image patches are extracted across the plurality of 2D image slices, wherein the spatial constraint is determined based on a spatial relationship of the plurality of 2D image slices.

11. A method for segmenting a biomedical image including at least one tree structure object, comprising:

receiving the biomedical image and a learning model, the biomedical image being acquired by an image acquisition device;

extracting, by at least one processor, a plurality of image patches from the biomedical image; and

applying, by the at least one processor, the learning model to the plurality of image patches to segment the biomedical image, wherein the learning model includes a convolutional network configured to process the plurality of image patches to construct respective feature maps and a tree structure network configured to process the feature maps collectively to obtain a segmentation mask for the tree structure object, wherein the tree structure network models a spatial constraint of the plurality of image patches.

12. The method of claim 11 , wherein extracting the plurality of image patches further includes:

determining a centerline of the tree structure object in the biomedical image; and

extracting the plurality of image patches along the centerline.

13. The method of claim 11 , wherein the convolutional network includes a plurality of fully convolutional networks each configured to process an image patch.

14. The method of claim 13 , wherein the plurality of fully convolutional networks process the plurality of image patches in parallel.

15. The method of claim 11 , wherein the tree structure network is a tree structure convolution recurrent neural network.

16. The method of claim 11 , wherein the spatial constraint is determined based on a tree structure of the image patches.

17. The method of claim 11 , wherein the spatial constraint is determined based on a spatial relationship between two neighboring image patches among the plurality of image patches.

18. The method of claim 11 , wherein the convolutional network and the tree structure network are trained jointly using a gradient descent based method.

19. The method of claim 11 , wherein the tree structure object is a blood vessel.

20. A non-transitory computer-readable medium having a computer program stored thereon, wherein the computer program, when executed by at least one processor, performs a method for segmenting a biomedical image including at least one tree structure object, the method comprising:

receiving the biomedical image and a learning model, the biomedical image being acquired by an image acquisition device;

extracting a plurality of image patches from the biomedical image; and

applying the learning model to the plurality of image patches to segment the biomedical image, wherein the learning model includes a convolutional network configured to process the plurality of image patches to construct respective feature maps and a tree structure network configured to process the feature maps collectively to obtain a segmentation mask for the tree structure object, wherein the tree structure network models a spatial constraint of the plurality of image patches.