DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1, 2, 11-16, 23, 25, 30, 54, 55, 63, 66, 73, 75, 168 and 168 is/are rejected under 35 U.S.C. 103 as being unpatentable over D1 (U.S. PG-PUB NO. 2024/0386998) in view of D2 (U.S. PG-PUB NO. 2024/0301493).
-Regarding claim 1, D1 discloses a computer-implemented method for image registration in primary analysis (novel registration technique to align two images, [0158]), comprising: wherein the polonies are obtained from flow cell images in one or more reference cycles (system determines one or more sequencing colonies (and optionally their properties such as amplitude, location, profile, brightness, background, saturated pixels) in each image tile of the plurality of reference images tiles, [0237]); generating, by the processor, one or more template images by registering the polonies to the one or more template images using the coordinates thereof (the system can generate and align two synthetic images corresponding to the images, [0158]; the system can insert an identical standard Gaussian profile at the location of each detected sequencing colony in the reference image tile, [0318]); obtaining, by the processor, a flow cell image in a cycle (At block 522, the system obtains a flow image. The flow image captures a region of interest on the substrate, [0240]); and determining, by the processor, a plurality of transformations of the flow cell image based on the one or more template images, each of the plurality of transformations corresponding to a subtile of the flow cell image and configured to register the subtile of the flow cell image to the one or more template images (the system divides the flow image divided into a plurality of image tiles, [0240]; the system registers a center sub-image of the flow image tile and a center sub-image of a reference image tile to obtain a global horizontal shift and a global vertical shift of the flow image tile with respect to the reference image tile, [0316]; correlating the first synthetic image with the second synthetic image comprises performing a two-dimensional cross correlation using Fourier transform, [0319]; shifted by a distance (gx, gy) (e.g., an affine transformation), [0320]).
D1 is silent to teaching that determining, by a processor, coordinates of polonies in a reference coordinate system. However, the claimed limitation is well known in the art as evidenced by D2.
In the same field of endeavor, D2 teaches determining, by a processor, coordinates of polonies in a reference coordinate system (the system assigns coordinate values of the first reference coordinate space to pixels of at least one of the first plurality of images, [0102]).
Therefore, it would have been obvious to one of ordinary skills in the art before the effective filing date of the claimed invention to combine the teaching of D1 with the teaching of D2 in order to express colony locations in a common reference coordinate system for cross-cycle registration (a predictable use of a known coordinate framework).
-Regarding claim 2, the combination further discloses obtaining image intensities, sizes, shapes, or their combinations of the polonies from a plurality of subtiles of the flow cell images in the one or more reference cycles (D1, the system determines one or more sequencing colonies (and optionally their properties such as amplitude, location, profile, brightness, background, saturated pixels) in each image tile of the plurality of reference images tiles, [0237]).
-Regarding claim 11, the combination further discloses registering, by the processor, subtiles of the flow cell image to the one or more template images using the plurality of transformations (D1, the system registers a center sub-image of the flow image tile and a center sub-image of a reference image tile to obtain a global horizontal shift and a global vertical shift, [0316]; D2, the system generates a coordinate transformation function between the first reference coordinate space and the second reference coordinate space based on the plurality of transformation parameters, [0121]).
-Regarding claim 12, the combination further discloses the one or more reference cycles includes one of [[the]]a first 5 cycles, and the cycle is different from the one or more reference cycles (D1, The method 500 comprises a process 502 for processing reference image(s) from one or more preamble or reference flows and a process 520 for processing flow images from a given flow step, [0234]; The preamble flow may result in multiple reference images, [0238]).
-Regarding claim 13, the combination further discloses the flow cell images are from 1 channel, or 2, 3, or 4 different channels (D1, The ring image can be a single-color image (e.g., greyscale image) or a color image, [0231]).
-Regarding claim 14, the combination further discloses some or all of the polonies are included in the flow cell image (D1, In each flow step, one or more flow images can be generated to capture the properties, for example signals, of the plurality of colonies on the substrate, [0240]).
-Regarding claim 15, the combination further discloses some or all of the polonies are included in the subtiles of the flow cell image (D1, each image tile (e.g., image tile 400 in FIG. 4) captures a plurality of sequencing colonies, [0232]).
-Regarding claim 16, the combination further discloses some or all of the polonies are included in selected regions in the subtiles of the flow cell image (D1, In the first synthetic image, each sequencing colony in the center sub-image is represented, [0317]).
-Regarding claim 23, the combination further discloses generating, by the processor, one or more transformed images of the one or more template images (D1, In each iteration, the system applies the affine transformation to the reference image or reference bead locations, [0321]).
-Regarding claim 25, the combination further discloses determining the plurality of transformations comprises: for each of the plurality of transformations, determining a corresponding cross correlation of a selected region of the subtile with the one or more template images (D1, the system registers a center sub-image of the flow image tile and a center sub-image of a reference image tile, [0316]; correlating the first synthetic image with the second synthetic image comprises performing a two-dimensional cross correlation using Fourier transform, [0319]).
-Regarding claim 30, the combination further discloses determining the plurality of transformations comprises: for each subtile, determining a shift, d, with a subpixel resolution, based on the corresponding cross correlation (D1, the system identifies a horizontal shift gx (i.e., x) and a vertical shift gy (i.e., y), in pixel units, which would produce the maximum overlap between the two synthetic images, [0319]; the initial location is a sub-pixel location, [0313]).
-Regarding claim 54, the combination further discloses providing, by the processor, a plurality of nucleic acid template molecules immobilized on a support, wherein each nucleic acid template molecule comprise an insert sequence (D1, Sequencing may be single molecule sequencing or sequencing by synthesis, for example. Sequencing may be performed using template nucleic acid molecules immobilized on a support, such as a flow cell or one or more beads on a substrate as described herein, [0174]; a sequencing library can be prepared, and sequencing adapters (e.g., adapter sequence 101 in FIG. 1) can be ligated to the ends of the individual nucleic acids, [0207]).
-Regarding claim 55, the combination further discloses generating, by a sequencing system, the flow cell images by conducting one or more cycles of sequencing reactions of the plurality of nucleic acid template molecules immobilized on the support (D1, involve a large number of flow cycles (e.g., hundreds, thousands, tens of thousands, hundreds of thousands, millions of flow cycles), with each flow cycle comprising multiple flow steps, [0231]; In each flow step, one or more flow images can be generated to capture the properties, for example signals, of the plurality of colonies on the substrate, [0240]).
-Regarding claim 63, the combination further discloses the flow cell images comprises optical signals emitted from nucleotide reagents bound to a unbalanced diversity of nucleotide bases of A, G, C and T/U among the plurality of nucleic acid template molecules immobilized on the support in the one or more cycles (D1, In each flow step, one or more flow images can be generated to capture the properties, for example signals, of the plurality of colonies on the substrate, [0240]; all colonies captured in the image contain the same count of the same nucleotide, [0236]).
-Regarding claim 66, the combination further discloses providing, by the processor, a cellular sample having a plurality of concatemer molecules immobilized on a support, wherein each concatemer molecule corresponds to a target RNA of a cellular sample (D2, performing in situ single-cell sequencing comprises using fluorescent in situ RNA sequencing (FISSEQ), circular templates are amplified by rolling circle amplification (RCA) followed by sequencing and imaging, [0062]; unique nucleic acid barcode sequences are added to a growing barcode concatemer attached, [0075]).
-Regarding claim 73, D1 discloses a computer-implemented system for image registration in primary analysis (novel registration technique to align two images, [0158]), comprising: one or more hardware processors (processor 1110, [0341]); one or more data storage devices storing instructions (storage 1140, [0341]) executable by the one or more hardware processors to cause the one or more hardware processors to perform operations, the operations comprising: wherein the polonies are obtained from flow cell images in one or more reference cycles (system determines one or more sequencing colonies (and optionally their properties such as amplitude, location, profile, brightness, background, saturated pixels) in each image tile of the plurality of reference images tiles, [0237]); generating one or more template images by registering the polonies to the one or more template images using the coordinates thereof (the system can generate and align two synthetic images corresponding to the images, [0158]; the system can insert an identical standard Gaussian profile at the location of each detected sequencing colony in the reference image tile, [0318]); obtaining a flow cell image in a cycle (At block 522, the system obtains a flow image. The flow image captures a region of interest on the substrate, [0240]); and determining a plurality of transformations of the flow cell image based on the one or more template images, each of the plurality of transformations corresponding to a subtile of the flow cell image and configured to register the subtile of the flow cell image to the one or more template images (the system divides the flow image divided into a plurality of image tiles, [0240]; the system registers a center sub-image of the flow image tile and a center sub-image of a reference image tile to obtain a global horizontal shift and a global vertical shift of the flow image tile with respect to the reference image tile, [0316]; correlating the first synthetic image with the second synthetic image comprises performing a two-dimensional cross correlation using Fourier transform, [0319]; shifted by a distance (gx, gy) (e.g., an affine transformation), [0320]).
D1 is silent to teaching that determining coordinates of polonies in a reference coordinate system. However, the claimed limitation is well known in the art as evidenced by D2.
In the same field of endeavor, D2 teaches determining coordinates of polonies in a reference coordinate system (the system assigns coordinate values of the first reference coordinate space to pixels of at least one of the first plurality of images, [0102]).
Therefore, it would have been obvious to one of ordinary skills in the art before the effective filing date of the claimed invention to combine the teaching of D1 with the teaching of D2 in order to express colony locations in a common reference coordinate system for cross-cycle registration (a predictable use of a known coordinate framework).
-Regarding claim 75, D1 discloses one or more non-transitory computer readable storage media (storage 1140, [0341]) encoded with instructions that, when executed by one or more hardware processors (processor 1110, [0341]), cause the one or more hardware processors to perform operations for image registration in primary analysis (novel registration technique to align two images, [0158]), the operations comprising: wherein the polonies are obtained from flow cell images in one or more reference cycles (system determines one or more sequencing colonies (and optionally their properties such as amplitude, location, profile, brightness, background, saturated pixels) in each image tile of the plurality of reference images tiles, [0237]); generating one or more template images by registering the polonies to the one or more template images using the coordinates thereof (the system can generate and align two synthetic images corresponding to the images, [0158]; the system can insert an identical standard Gaussian profile at the location of each detected sequencing colony in the reference image tile, [0318]); obtaining a flow cell image in a cycle (At block 522, the system obtains a flow image. The flow image captures a region of interest on the substrate, [0240]); and determining a plurality of transformations of the flow cell image based on the one or more template images, each of the plurality of transformations corresponding to a subtile of the flow cell image and configured to register the subtile of the flow cell image to the one or more template images (the system divides the flow image divided into a plurality of image tiles, [0240]; the system registers a center sub-image of the flow image tile and a center sub-image of a reference image tile to obtain a global horizontal shift and a global vertical shift of the flow image tile with respect to the reference image tile, [0316]; correlating the first synthetic image with the second synthetic image comprises performing a two-dimensional cross correlation using Fourier transform, [0319]; shifted by a distance (gx, gy) (e.g., an affine transformation), [0320]).
-Regarding claim 168, the combination further dioceses the polonies are of an in situ sample of one or more cells or tissue (D2, performing in situ single-cell sequencing comprises using fluorescent in situ RNA sequencing (FISSEQ), [0062]; for identifying neuronal single cells in a readout image, [0162]).
-Regarding claim 169, the combination further discloses the polonies are of one or more samples of unbalanced diversity nucleotide bases in one or more cycles of a sequencing run (D1, all colonies captured in the image contain the same count of the same nucleotide, [0236]).
Claim(s) 3 is/are rejected under 35 U.S.C. 103 as being unpatentable over D1 (U.S. PG-PUB NO. 2024/0386998) in view of D2 (U.S. PG-PUB NO. 2024/0301493) and further in view of D3 (U.S. PG-PUB NO. 2017/0160535).
-Regarding claim 3, the combination is silent to teaching that determining the coordinates of the polonies in the reference coordinate system is based on one or more fiducial markers external to the flow cell images in the one or more reference cycles and the flow cell image in the cycle. However, the claimed limitation is well known in the art as evidenced by D3.
In the same field of endeavor, D3 teaches determining the coordinates of the polonies in the reference coordinate system is based on one or more fiducial markers external to the flow cell images in the one or more reference cycles and the flow cell image in the cycle (provide reference points on sections cut from the block so that a coordinate system can be established and used for mapping positions on a section, [0116]).
Therefore, it would have been obvious to one of ordinary skills in the art before the effective filing date of the claimed invention to combine the teaching of the combination with the teaching of D3 in order to anchor polony coordinates to a single stable reference coordinate system that is common across the reference cycles and the flow cycle image (a known and predictable registration aid (extrinsic fiducials for cross-image coordinate registration), yielding the predictable result of consistent coordinates for accurate registration.
Allowable Subject Matter
Claim 32 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Claim 77 is allowed.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PING Y HSIEH whose telephone number is (571)270-3011. The examiner can normally be reached Monday-Friday, 9am-4pm.
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/PING Y HSIEH/ Primary Examiner, Art Unit 2664
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