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"Method and System for Binary and Quasi-Binary Atlas-Based Auto-Contouring of Volume Sets in Medical Images" in Patent Application Approval Process

July 3, 2014



By a News Reporter-Staff News Editor at Politics & Government Week -- A patent application by the inventors Tizhoosh, Hamid Reza (Aurora, CA); Khalvati, Farzad (Richmond Hill, CA), filed on April 13, 2012, was made available online on June 19, 2014, according to news reporting originating from Washington, D.C., by VerticalNews correspondents.

This patent application has not been assigned to a company or institution.

The following quote was obtained by the news editors from the background information supplied by the inventors: "Atlas-based segmentation (ABS) is a well-established and widely used technique for extracting contours in medical images. Generally, ABS is a commonly used method for segmenting medical images. An atlas contains the locations and shapes of organs and/or lesions along with the spatial relationships between them. There are different commonly-used ways to generate an atlas, including: (i) an expert manually segments selected images; or (ii) software generates an atlas by reading and processing multiple segmented images (from one or multiple experts). When an atlas is available then new (unseen) images can be contoured and/or segmented by mapping their coordinate space to that of the atlas, such that the anatomical boundaries are correctly marked (a process called image registration). In the registration process the images in the atlas are registered against the new image. The registered images are then compared against the new image to find the best matching registered image. Afterward, the corresponding image transformation, obtained by the registration process, is applied to the contour of the best matching image. The contour is then deformed and mapped to the new image.

"The accuracy of the ABS mainly depends on two factors: (i) the size of the atlas; and (ii) the performance of image registration. Large atlases (meaning atlases that comprise one or multiple atlases) and sophisticated registration algorithms can be employed to increase the accuracy of the contouring. However, using large and comprehensive atlases can reduce computational efficiency such that the results can be provided after long searching and registration times.

"Prior art ABS systems and methods are disclosed in the following prior art references: U.S. Pat. No. 6,901,156 having the title METHOD, SYSTEM AND COMPUTER READABLE MEDIUM FOR AN INTELLIGENT SEARCH WORKSTATION FOR COMPUTER ASSISTED INTERPRETATION OF MEDICAL IMAGES;

"U.S. Pat. No. 6,950,544 having the title AUTOMATED MEASUREMENT OF ANATOMICAL STRUCTURES IN MEDICAL IMAGING;

"U.S. Pat. No. 7,245,766 having the title METHOD AND APPARATUS FOR DETERMINING A REGION IN AN IMAGE BASED ON A USER INPUT;

"U.S. Pat. No. 7,324,842 having the title ATLAS AND METHODS FOR SEGMENTATION AND ALIGNMENT OF ANATOMICAL DATA;

"U.S. Pat. No. 7,324,842 having the title ATLAS AND METHODS FOR SEGMENTATION AND ALIGNMENT OF ANATOMICAL DATA;

"U.S. Pat. No. 7,327,138 having the title METHOD FOR GENERATING AN MR ATLAS AND FOR MR IMAGING USING SAME;

"U.S. Pat. No. 7,333,644 having the title SYSTEMS AND METHODS FOR PROVIDING AUTOMATIC 3D LESION SEGMENTATION AND MEASUREMENTS;

"U.S. Pat. No. 7,340,082 having the title METHOD AND MEDICAL IMAGING APPARATUS FOR DETERMINING A SLICE IN AN EXAMINATION VOLUME FOR DATA ACQUISITION IN THE SLICE;

"U.S. Pat. No. 7,346,201 having the title SEMI-AUTOMATED MEASUREMENT OF ANATOMICAL STRUCTURES USING STATISTICAL AND MORPHOLOGICAL PRIORS;

"U.S. Pat. No. 7,394,946 having the title METHOD FOR AUTOMATICALLY MAPPING OF GEOMETRIC OBJECTS IN DIGITAL MEDICAL IMAGES;

"U.S. Pat. No. 7,584,080 having the title CONSTRUCTING A STATISTICAL SHAPE MODEL FROM TWO-DIMENSIONAL OR THREE-DIMENSIONAL DATA;

"U.S. Pat. No. 7,623,709 having the title METHOD AND SYSTEM FOR SEGMENTING IMAGE DATA;

"U.S. Pat. No. 7,646,898 having the title METHODS AND APPARATUS FOR PROCESSING MEDICAL IMAGES;

"U.S. Pat. No. 7,773,786 having the title METHOD AND APPARATUS FOR THREE-DIMENSIONAL INTERACTIVE TOOLS FOR SEMI-AUTOMATIC SEGMENTATION AND EDITING OF IMAGE OBJECTS;

"U.S. Pat. No. 7,792,348 having the title METHOD AND APPARATUS OF USING PROBABILISTIC ATLAS FOR CANCER DETECTION;

"U.S. Pat. No. 7,817,836 having the title METHODS FOR VOLUMETRIC CONTOURING WITH EXPERT GUIDANCE;

"U.S. Pat. No. 7,822,244 having the title SEGMENTING MEDICAL IMAGE DATA SETS;

"U.S. Pat. No. 7,822,291 having the title NON-RIGID MULTI-MODAL REGISTRATION USING STATISTICAL LEARNING METHODS;

"U.S. Pat. No. 7,831,079 having the title SEGMENTATION OF ANATOMIC STRUCTURES USING NAVIGATION TABLE;

"U.S. Patent Application Publication No. 20030139659 having the title ATLAS AND METHODS FOR SEGMENTATION AND ALIGNMENT OF ANATOMICAL DATA;

"U.S. Patent Application Publication No. 20030228042 having the title METHOD AND SYSTEM FOR PREPARATION OF CUSTOMIZED IMAGING ATLAS AND REGISTRATION WITH PATIENT IMAGES;

"U.S. Patent Application Publication No. 20050031202 having the title IMAGE REGION SEGMENTATION SYSTEM AND METHOD;

"U.S. Patent Application Publication No. 20050069183 having the title SEMI-AUTOMATED MEASUREMENT OF ANATOMICAL STRUCTURES USING STATISTICAL AND MORPHOLOGICAL PRIORS;

"U.S. Patent Application Publication No. 20080267468 having the title SYSTEM AND METHOD FOR SEGMENTING A REGION IN A MEDICAL IMAGE;

"U.S. Patent Application Publication No. 20090226060 having the title METHOD AND SYSTEM FOR IMPROVED IMAGE SEGMENTATION;

"U.S. Patent Application Publication No. 20100266170 having the title METHODS AND SYSTEMS FOR FULLY AUTOMATIC SEGMENTATION OF MEDICAL IMAGES;

"U.S. Patent Application Publication No. 20100286995 having the title INTERACTIVE ATLAS TO IMAGE REGISTRATION;

"U.S. Patent Application Publication No. 20100295848 having the title INTERACTIVE IMAGE SEGMENTATION;

"U.S. Patent Application Publication No. 20110013818 having the title 3D MEDICAL IMAGE SEGMENTATION;

"U.S. Patent Application Publication No. 20090297014 having the title SYSTEM FOR ASSESSING RADIATION TREATMENT PLAN SEGMENTATIONS; and

"U.S. Patent Application Publication No. 20090226060 having the title METHOD AND SYSTEM FOR IMPROVED IMAGE SEGMENTATION."

In addition to the background information obtained for this patent application, VerticalNews journalists also obtained the inventors' summary information for this patent application: "In one aspect, the present disclosure relates to a method of QB-Code generation to efficiently use atlas-based segmentation using any of binary or quasi-binary representations of image regions of interest, or a combination of binary and quasi-binary representation of image regions of interest, said method characterized in that it comprises the following steps: identifying one or more regions of interest in an image; generating a QB-code for the one or more regions of interest by searching to identify an applicable QB-Code in any of the following: a binary atlas; or a quasi-binary atlas; and determining a gold standard contour, said gold standard contour being attached to the generated QB-Code.

"Said method characterized in that it may comprise the further step of generating the QB-Code in accordance with one or more of the following schemes: a pure binary atlas segmentation; a quasi-binary atlas segmentation; a binary controlled atlas segmentation; or a quasi-binary controlled atlas segmentation.

"Said method characterized in that it may comprise the further step of atlas segmentation with registration of QB-Codes.

"The method characterized in that it may comprise the further step of utilizing the QB-Code and apply sequential edit propagation to achieve fast slice-by-slice auto-contouring of volume image data.

"Said method characterized in that it may comprise the further step of achieving fast slice-by-slice auto-contouring of volume image data by the following steps of: generating or receiving a slice of the ROI as a contoured ROI; and repeating the following steps until all images are processed: editing the contoured ROI and inserting the edited contoured ROI and the associated QB-code into the binary and/or quasi-binary atlas; and automatically segmenting a next slice by propagating the contoured ROI and an associated gold standard contour.

"Said method characterized in that it may comprise one or more of the further following steps: inserting the edited contoured ROI into a binary atlas; inserting the edited contoured ROI into a quasi-binary atlas; inserting the edited contoured ROI into a binary controlled atlas; or inserting the edited contoured ROI into a quasi-binary controlled atlas.

"Said method characterized in that it may comprise the further step of generating the QB-Code by one or more of the following steps: thresholding the ROI; thresholding to transform the ROI; thresholding to segment the ROI; generating a local binary pattern involving the ROI; and generating a customized binary code involving the ROI.

"Said method characterized in that it may comprise the further step of generating the QB-Code by one or more of the following steps: (multi-) thresholding the ROI; (multi-) thresholding to transform the ROI; (multi-) thresholding to segment the ROI; generating a local binary pattern involving the ROI; and generating a customized binary code involving the ROI.

"Said method characterized in that it may comprise the further following steps: creating the binary atlas or quasi-binary atlas; grouping atlas entries; generating one or more representative samples for each group of atlas entries; and repeating the following steps until QB-Code is generated for each of the one or more representative samples for each group: generating QB-Code for each of the one or more representative samples for each group; and querying whether QB-Code is generated for each group.

"Said method characterized in that it may comprise the further step of creating the binary atlas or quasi-binary atlas to generate a pure QBinary atlas, or a QBinary controlled atlas.

"Said method characterized in that it may comprise the further step of utilizing an image registration algorithm for QB-Code generation.

"Said method characterized in that it may comprise the further step of registering the QB-Codes.

"In another aspect, the present disclosure relates to a system of QB-Code generation to efficiently implement atlas-based segmentation using any of binary or quasi-binary representations of image regions of interest, or a combination of binary and quasi-binary representation of image regions of interest, said system characterized in that it comprises: one or more images with contours; a QB-Code Generator operable to receive the one or more images and a number of bits, and to utilize the one or more images and number of bits to generate QB-Code; and an atlas creation means operable to receive atlas type input and to generate an atlas.

"Said system characterized in that it may further comprise the atlas creation means being operable to generate the atlas as a binary atlas or as a QBinary-controlled atlas.

"Said system characterized in that it may further comprise the QB-Code Generator being operable to identify one or more regions of interest (ROI) in the one or more images and to use the ROI in the generation of QB-Code.

"Said system characterized in that it may further comprise a display means, whereby contour of the one or more images are displayable to a user.

"Said system characterized in that it may further comprise an atlas search means operable to perform an atlas search.

"Said system characterized in that it may further comprise one or more training modes.

"Said system characterized in that it may further comprise one or more of the following: an atlas creation training mode involving sequential processing of a list of images; and an atlas creation training mode involving grouping of similar samples.

"Said system characterized in that it may further comprise a means for segmenting images operable in an interactive mode.

"In this respect, before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not limited in its application to the details of construction and to the arrangements of the components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced and carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein are for the purpose of description and should not be regarded as limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

"The invention will be better understood and objects of the invention will become apparent when consideration is given to the following detailed description thereof. Such description makes reference to the annexed drawings wherein:

"FIG. 1 shows an example of prior art atlas creation.

"FIG. 2 shows an example of QB-code generation of an embodiment of the present invention.

"FIG. 3 shows an example of QB-code generation of an embodiment of the present invention.

"FIG. 4 shows an example of QBinary atlas creation of an embodiment of the present invention.

"FIG. 5 shows an example of pure QBinary (just binary) atlas segmentation of an embodiment of the present invention.

"FIG. 6 shows an example of QBinary controlled atlas creation of an embodiment of the present invention.

"FIG. 7 shows an example of QBinary controlled atlas segmentation of an embodiment of the present invention.

"FIG. 8 shows an example of Fast Slice-by-Slice Auto-Contouring of Volume Data (SbS ACV) of an embodiment of the present invention.

"FIG. 9 shows a table that provides examples of different schemes for generation of a QB-Code of an embodiment of the present invention.

"FIG. 10 shows an example of an overall picture for atlas creation (QBinary or QBinary-controlled) of an embodiment of the present invention.

"FIG. 11 shows an example of an overall picture using QBinary or QBinary-controlled atlas-based segmentation of an embodiment of the present invention.

"FIG. 12 shows a table that provides results of the clinical validation for segmentation of prostate gland in magnetic resonance images using an embodiment of the present invention.

"FIG. 13 shows examples of ROI and the corresponding QBinary codes of an embodiment of the present invention.

"In the drawings, embodiments of the invention are illustrated by way of example. It is to be expressly understood that the description and drawings are only for the purpose of illustration and as an aid to understanding, and are not intended as a definition of the limits of the invention."

URL and more information on this patent application, see: Tizhoosh, Hamid Reza; Khalvati, Farzad. Method and System for Binary and Quasi-Binary Atlas-Based Auto-Contouring of Volume Sets in Medical Images. Filed April 13, 2012 and posted June 19, 2014. Patent URL: http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&u=%2Fnetahtml%2FPTO%2Fsearch-adv.html&r=3922&p=79&f=G&l=50&d=PG01&S1=20140612.PD.&OS=PD/20140612&RS=PD/20140612

Keywords for this news article include: Patents.

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Source: Politics & Government Week


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