Abstract:
Certain aspects of an apparatus and method for orienting tissue samples for comparison may include incrementally rotating orientation of a first image by a predetermined rotation angle while maintaining orientation of a second image at a fixed angle, checking alignment of the orientation of the first image with the orientation of the second image at each predetermined rotation angle by matching a plurality of points in the first image and the second image, determining whether a predetermined rotation angle is a correct rotation angle for alignment based on a count of the plurality of points being greater than a threshold value and rotating to the next predetermined rotation angle when the count of the plurality of points is less than or equal to a threshold value.

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS/INCORPORATION BY REFERENCE 
     This application makes reference to: 
     Commonly assigned U.S. patent application Ser. No. 13/671,143 filed on Nov. 7, 2012 and commonly assigned U.S. patent application Ser. No. 13/410,960 filed on Mar. 2, 2012. 
     Each of the above referenced applications is hereby incorporated herein by reference in its entirety. 
     FIELD 
     Certain embodiments of the disclosure relate to pathology imaging. More specifically, certain embodiments of the disclosure relate to a method and apparatus for orienting tissue samples for image comparison. 
     BACKGROUND 
     Histology is the study of the microscopic anatomy of tissues and is essential in diagnosing disease, developing medicine and many other fields. In histology, thin slices of tissue samples, typically adjacent samples, are examined and compared under a light microscope or electron microscope. Often, however, a slide might contain the tissue sample in any portion of the slide and the slide may be oriented in different ways due to variable layouts of different digital pathology systems, causing difficulty in accurate location of the target area on a slide. When different slices from the tissue sample are prepared separately for staining by different technicians, the orientation of the slices is often altered in arbitrary ways. Manual estimation and manual reorientation must be performed by pathology analysts to properly compare adjacent tissue slices, often resulting in analyst error and inaccurate results. 
     Therefore there is a need in the art for a method and apparatus for orienting tissue samples for image comparison in digital pathology. 
     Further limitations and disadvantages of conventional and traditional approaches will become apparent to one of skill in the art, through comparison of such systems with some aspects of the present disclosure as set forth in the remainder of the present application with reference to the drawings. 
     SUMMARY 
     An apparatus and/or method is provided for orienting tissue samples for image comparison in digital pathology substantially as shown in and/or described in connection with at least one of the figures, as set forth more completely in the claims. 
     These and other features and advantages of the present disclosure may be appreciated from a review of the following detailed description of the present disclosure, along with the accompanying figures in which like reference numerals refer to like parts throughout. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a block diagram illustrating an orientation module in accordance with an embodiment of the disclosure; 
         FIG. 2  is a block diagram of a computer system for implementing the orientation module  100  in accordance with embodiments of the present invention; 
         FIG. 3  is an illustration of a flow diagram for a method for orienting a digital pathology image according to exemplary embodiments of the present invention; and 
         FIG. 4  is an illustration of a flow diagram for a method for orienting a digital pathology image according to exemplary embodiments of the present invention. 
     
    
    
     DETAILED DESCRIPTION 
     Certain implementations may be found in an apparatus and/or method for orienting tissue samples for image comparison. According to one embodiment, a first tissue sample image is rotated incrementally. At each rotation, the first tissue sample image is compared to a comparison image to determine a number of matching points between the two images, as discussed in the U.S. patent application Ser. No. 13/410,960 filed on Mar. 2, 2012, entitled “Automatic pathological image alignment and view synchronization for stain images.” If the number of matching points is less than a particular threshold value, the first time sample image is incrementally rotated to a next predetermined rotation angle. The tissue sample image is incrementally rotated until the number of matching points between the first tissue sample image and the comparison image is above a predetermined threshold value, at which point in time the two images will be considered aligned. 
       FIG. 1  is a block diagram illustrating an orientation module  100  in accordance with an embodiment of the disclosure. The orientation module  100  comprises a background module  102 , an alignment module  104 , and a rotation module  106 . The identification module  100  takes an input slide image  101  and an input comparison image  103  as input. According to some embodiments, the input slide image  101  is a digital pathology image which is stained with one or more various color dyes to enhance cellular visibility. The input comparison image  103  is also a digital pathology image from a different slide source that may also be stained with one or more various color dyes. 
     In one embodiment, the input slide image  101  may be an Immunohistochemistry (IHC) stained image. IHC refers to the process of detecting antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues. According to one embodiment, the input comparison image  103  is a Hematoxylin and eosin (H&amp;E) stained image. The H&amp;E staining method involves application of hemalum, which is a complex formed from aluminum ions and oxidized haematoxylin. This colors the nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The nuclear staining is followed by counterstaining with an aqueous or alcoholic solution of eosin Y, which colors other structures, such as eosinophilic structures, in various shades of red, pink and orange 
     The input slide image  101  is first divided by the background module  102  into a background and a foreground using estimation techniques discussed in U.S. patent application Ser. No. 13/410,960 filed on Mar. 2, 2012. Then, the input image  101  is rotated by the rotation module  106  to a next predetermined angle. According to one embodiment, the rotational module  106  rotates the input image  101  by ten degrees in a negative or positive direction to the next predetermined rotation angle Θ. In other embodiments, other predetermined angle increments are utilized. 
     The alignment module  104  performs point matching alignment between the input slide image  101  and the input comparison image  103  as described in U.S. patent application Ser. No. 13/410,960 filed on Mar. 2, 2012. The alignment module  104  first performs segmentation on the input image  101 , by partitioning the input region into sub-regions so that within each region there is a homogeneous distribution of image contrast, also discussed in U.S. patent application Ser. No. 13/410,960 filed on Mar. 2, 2012. Structure-centered image partitioning is performed on the comparison image  103 . Then, key-points are generated for the segmented image  101  and the partitioned image  103 . Next, incremental cross matching and integration is performed with respect to both images  101  and  103 . Filtering, as disclosed in U.S. patent application Ser. No. 13/410,960, is performed on the cross-matched points, and a number of matching points are output. 
     Finally, the rotation module  106  determines whether the current rotation has aligned the input image  101  and the input comparison image  103 . According to one embodiment, if the amount of matching points exceeds forty, the rotation angle Θ is determined to be the correct alignment rotation angle to be used to align the input image  101  and the comparison image  103 . If the number of matching points does not exceed, for example, 40, then the rotation module rotates the input image  101  by a predetermined incremental angle and the alignment module  104  is triggered to again perform point matching alignment, until an incremental angle found is determined to be the correct alignment rotation angle which results in alignment of the input image  101  and the comparison image  103 . 
     Once the aligning rotation angle Θ is found, the orientation module  100  outputs an aligned image  110  which has corresponding matching points to the input comparison image  103  that exceed a predetermined amount. 
       FIG. 2  is a block diagram of a computer system  200  for implementing the orientation module  100  in accordance with embodiments of the present invention. The computer system  200  includes a processor  202 , a memory  204  and various support circuits  206 . The processor  202  may include one or more microprocessors known in the art, and/or dedicated function processors such as field programmable gate arrays programmed to perform dedicated processing functions. The support circuits  206  for the processor  202  include microcontrollers, application specific integrated circuits (ASIC), cache, power supplies, clock circuits, data registers, input/output (I/O) interface  208 , and the like. The I/O interface  208  may be directly coupled to the memory  204  or coupled through the supporting circuits  206 . The I/O interface  208  may also be configured for communication with input devices and/or output devices  210 , such as, network devices, various storage devices, mouse, keyboard, displays, sensors and the like. 
     The memory  204  stores non-transient processor-executable instructions and/or data that may be executed by and/or used by the processor  202 . These processor-executable instructions may comprise firmware, software, and the like, or some combination thereof. Modules having processor-executable instructions that are stored in the memory  204  comprise the orientation module  220 , further comprising the background module  222 , the rotation module  226 , and the alignment module  224 . 
     The computer  200  may be programmed with one or more operating systems (generally referred to as operating system (OS)  214 , which may include OS/2, Java VIRTUAL MACHINE, LINUX, SOLARIS, UNIX, HPUX, AIX, WINDOWS, WINDOWS95, WINDOWS98, WINDOWS NT, WINDOWS 2000, WINDOWS ME, WINDOWS XP, WINDOWS SERVER, among other known platforms. At least a portion of the operating system  214  may be disposed in the memory  204 . In an exemplary embodiment, the memory  204  may include one or more of the following: random access memory, read only memory, magneto-resistive read/write memory, optical read/write memory, cache memory, magnetic read/write memory, and the like, as well as signal-bearing media, not including non-transitory signals such as carrier waves and the like. 
       FIG. 3  is an illustration of a flow diagram for a method  300  for orienting a digital pathology image according to exemplary embodiments of the present invention. The method  300  is an implementation of the orientation module  100  shown in  FIG. 1 , implemented as the orientation module  220  in  FIG. 2  as executed by the processor  202 . The method begins at step  302  and proceeds to step  304 . 
     At step  304 , the rotation module  226  rotates an input image incrementally to a subsequent predetermined rotation angle. According to some embodiments, the rotation module  206  rotates the input image by +/−10.0 degree increments, though the present embodiment is not restricted to 10.0 degree increments and other rotational increments could be used. 
     The method then moves to step  306 , where the alignment module  224  performs point matching alignment between the input image and a comparison image, as briefly discussed above. The alignment procedure is discussed in greater detail in conjunction with  FIG. 4  and is also fully disclosed in the U.S. patent application Ser. No. 13/410,960 filed on Mar. 2, 2012. 
     At step  308 , a number of matching points are determined. If at step  310  the number of matching points is greater than a threshold value, the method  030  proceeds to step  312 . At step  312 , the orientation of the input image  101  is verified as aligning with the comparison image  103 . The method ends at step  318 . 
     If the number of points that match is less than a threshold value, then the method  300  moves to step  304  so as to rotate the image by another increment to the next predetermined rotation angle. The method  300  then iterates until a rotation angle has been determined that results in alignment of the input image  101  and the comparison image  103 , at which point the method ends at step  318 . 
       FIG. 4  is an illustration of a flow diagram for a method  400  for orienting a digital pathology image according to exemplary embodiments of the present invention. The method  400  is an implementation of the alignment module  104  shown in  FIG. 1 , implemented as the alignment module  224  in  FIG. 2  as executed by the processor  202 . The method begins at step  402  and proceeds to step  404 . 
     At step  404 , the alignment module  224  segments the input image into a plurality of segments. At step  405 , the comparison image is partitioned by the alignment module  224 . Key-points are generated for the segments of the input image in step  406 . At step  408 , the key-points in the segments are matched with the partitioned comparison image. Finally, at step  410 , the matched segments are filtered. The method ends at step  412 . 
     Accordingly, the present disclosure may be realized in hardware, or a combination of hardware and software. The present disclosure may be realized in a centralized fashion in at least one computer system or in a distributed fashion where different elements may be spread across several interconnected computer systems. Any kind of computer system or other apparatus adapted for carrying out the methods described herein may be suited. A combination of hardware and software may be a general-purpose computer system with a computer program that, when being loaded and executed, may control the computer system such that it carries out the methods described herein. The present disclosure may be realized in hardware that comprises a portion of an integrated circuit that also performs other functions. 
     The present disclosure may also be embedded in a computer program product, which comprises all the features enabling the implementation of the methods described herein, and which when loaded in a computer system is able to carry out these methods. Computer program in the present context means any expression, in any language, code or notation, of a set of instructions intended to cause a system having an information processing capability to perform a particular function either directly or after either or both of the following: a) conversion to another language, code or notation; b) reproduction in a different material form. 
     While the present disclosure has been described with reference to certain embodiments, it will be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the scope of the present disclosure. In addition, many modifications may be made to adapt a particular situation or material to the teachings of the present disclosure without departing from its scope. Therefore, it is intended that the present disclosure not be limited to the particular embodiment disclosed, but that the present disclosure will include all embodiments falling within the scope of the appended claims.