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 .
In amendments dated 01/22/2026, applicant(s) amended claims 1, 11, 14 and 17 – 19. Claims 1 – 29 are still pending in this application.
Response to Arguments
Applicant’s arguments with respect to claims 1 - 29 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 01/22/026 was filed in compliance with the provisions of 37 CFR 1.97 and 1.98. Accordingly, the information disclosure statement is being considered by the examiner.
Applicants have not provided an explanation of relevance of cited document(s) discussed below.
Eskra et al. (U.S Patent No. 7,829,162 B2) teaches a thermal transfer printing medium that contains a thermal transfer layer which contains a first taggant and colorant, wherein: the first taggant comprises a fluorescent compound with an excitation wavelength selected from the group consisting of wavelengths of less than 400 nanometers, wavelengths of greater than 700 nanometers. When the thermal transfer layer is printed onto a white polyester substrate with a gloss of at least about 84, a surface smoothness Rz value of 1.2, and a reflective color represented by a chromaticity (a) of 1.91 and (b) of -6.79 and a lightness (L) of 95.63, when expressed by the CIE Lab color coordinate system, and when such printing utilizes a printing speed of 2.5 centimeters per second and a printing energy of 3.2 joules per square centimeter, a printed substrate with certain properties is produced. The printed substrate has a reflective color represented by a chromaticity (a) of from -15 to 15 and (b) from -18 to 18, and the printed substrate has a lightness (L) of less than about 35, when expressed by the CIE Lab color coordinate system. When the printed substrate is illuminated with light source that excites the first taggant with an excitation wavelength selected from the group consisting of wavelengths of less than 400 nanometers, wavelengths greater than 700 nanometers, the printed substrate produces a light fluorescence with a wavelength of from about 300 to about 700 nanometers.
Visscher et al. (U.S Patent No. 12099175 B2) teaches an adapter configured to be optically coupled to a plurality of microscopes and including a) a first microscope interface configured to optically couple a first microscope to an optical element in optical communication with an optical probe; b) a second microscope interface configured to optically couple a second microscope to the optical element in optical communication with the optical probe; and c) an optical arrangement configured to direct light collected from a sample with the aid of the optical probe to (1) the first microscope and second microscope simultaneously, or (2) the first microscope or second microscope selectively.
Schoenborn et al. (U.S PreGrant Publication No. 2015/0069268 A1) teaches a device for multi-photon fluorescence microscopy for obtaining information from biological tissue has a laser unit for generating an excitation radiation, an optical unit implemented for focusing the excitation radiation for generating an optical signal at various locations in or on an object to be investigated, and a detector module for capturing the optical signal from the region of the object. The optical unit is thereby displaceable at least in one direction relative to the object for generating the optical signal at various locations in or on the object. The invention further relates to a method for multi-photon fluorescence microscopy. In said manner, a device and a method for multi-photon fluorescence microscopy are provided for obtaining information from biological tissue, allowing recording of section images in an object with a large field of view, and thereby are simply constructed and reliable in operation.
Craighead et al. (U.S PreGrant Publication No. 2016/0032380 A1) is related to compositions, methods, and uses for obtaining sequence information from nucleic acid molecules.
Metzker et al. (U.S PreGrant Publication No. 20170349939 A1) provides methods and compositions for the detection of target nucleic acids using target reporter constructs (TRCs) which comprise target sequences complementary to the target nucleic acid. Further provided are methods of replicating the TRCs using rolling circle replication and/or rolling circle amplification to produce replicated TRCs which can be detected using probe sequences within the replicated TRCs.
Rulison et al. (U.S PreGrant Publication No. 2017/0167979 A1) is related to an apparatus, systems and methods for use in analyzing discrete reactions are provided. The analytical devices of the invention use an array of nanoscale regions (a chip) that has discrete patches, for example, patches of nanoscale regions. In some embodiments an analytical system is provided that has an analysis chip with an array of patches, each of the patches comprising nanoscale regions that emit fluorescent light when illuminated. The system has a two-dimensional (x, y) array of dichroic prisms, each prism comprising a dichroic element that diverts illumination light up in the z dimension of the array to a patch on the analysis chip above it. Each dichroic element transmits fluorescent light emitted by the patch that it illuminates, whereby the emitted light from each patch passes down through each dichroic prism. The analytical system also has a detector below the array of dichroic prisms that detects the transmitted fluorescent light. Such systems are useful for monitoring many analytical reactions at one time including single molecule sequencing reactions.
Trintchouk et al. (U.S PreGrant Publication No. 2024/0037744 A1 or U.S Patent No. ) teaches detecting pattern on max projection, intra-align channels, generate grid(s), associate the generated grid(s); and apply chromatic correction to grid locations.
Garcia et al. (U.S PreGrant Publication No. 2025/0148603 A1) provides related U.S Application data wherein teaches methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies; Garcia, by itself, can be considered prior art.
Trintchouk et al. (U.S Patent No. 11,900595 B2), in which can be used as alternate prior art, provides a method of quantifying features in a repeating pattern. In a non-limiting example, the method includes the steps of: obtaining an image of an object using a detection apparatus, wherein the image includes a repeating pattern of features having different signal levels; providing the image or image-related data to a computer, wherein the computer has parameter data that describe the repeating pattern of features; partitioning the image or the image-related data into a plurality of registration subimages on the computer; detecting on the computer the repeating pattern of features for each registration subimage and assigning an index address for each feature of the repeating pattern of features; and quantifying a signal level of each feature. The method can further include a step of providing the object wherein the object has a repeating pattern of features in a two-dimensional plane, such as a plane. The method can further include a step of providing the object wherein the object has a repeating pattern of features in one or more two-dimensional planes, such as a z-stack of single two-dimensional planes.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1 - 18 are rejected under 35 U.S.C. 103 as being unpatentable over Trintchouk et al. (U.S PreGrant Publication No. 2021/0350533 A1, previously cited in an Office Action dated 09/25/2025, hereinafter ‘Trintchouk’) in view of Price (U.S PreGrant Publication No. 2015/0206315 A1, hereinafter ‘Price’).
With respect to claim 1, Trintchouk teaches a method of quantifying features in a repeating pattern of an object (i.e., a method of quantifying features in a repeating pattern of an object, ¶0005), the method comprising: obtaining a plurality of images of the object using a detection apparatus (i.e., obtaining a plurality of images of the object using a detection apparatus, ¶0005); wherein the plurality of images includes a repeating pattern of features having different signal levels (i.e., wherein the image includes a repeating pattern of features having different signal levels, ¶0005); providing the images or image-related data to a computer, wherein the computer has parameter data that describe the repeating pattern of features (i.e., providing the image or image-related data to a computer, wherein the computer has parameter data that describe the repeating pattern of features, ¶0005); partitioning the image or the image-related data into a plurality of registration subimages on the computer (i.e., partitioning the image or the image-related data into a plurality of registration subimages on the computer, ¶0005); detecting on the computer the repeating pattern of features for each registration subimage (detecting on the computer the repeating pattern of features for each registration subimage, ¶0005); assigning an index address for each feature of the repeating pattern of features (i.e., assigning an index address for each feature of the repeating pattern of features, ¶0005); and quantifying a signal level of each feature (i.e., and quantifying a signal level of each feature, ¶0005), but fails to teach that said detecting is based on a correlation between at least an image of the plurality of images and a corrugation image associated with the parameter data.
However, in the same field of endeavor of partitioning image(s) and assigning value(s), the mentioned claimed limitations are well known in the art as evidenced by Price. In general, Price teaches detecting based on a correlation between at least an image of the plurality of images and a corrugation image associated with the parameter data (e.g., wherein identifying/finding is based on a comparison (e.g., difference or similarities) between an image from the plurality of image and an image linked to parameter (e.g. pixels), abstract, ¶0004, ¶0024 - ¶0025, ¶0028 - ¶0030, ¶0041, ¶0046, ¶0053 Fig. 2).
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention was made to modify the method of Trintchouk as taught by Price since Price suggested within abstract, ¶0004, ¶0024 - ¶0025, ¶0028 - ¶0030, ¶0041, ¶0046, ¶0053 Fig. 2 that such modification would improve accuracy and/or efficiency of between images in order to reduce processing time.
With respect to claim 2, Trintchouk in view of Price teaches the method of claim 1, wherein the signals are fluorescent intensities (i.e., signals are fluorescent intensities, ¶0036, ¶0055).
With respect to claim 3, Trintchouk in view of Price teaches the method of claim 1, further comprising providing the object, wherein the object has a repeating pattern of features in a two-dimensional plane (e.g., providing the object, wherein the object has a repeating pattern of features in a two-dimensional plane, ¶0005, claim 2).
With respect to claim 4, Trintchouk in view of Price teaches the method of claim 3, wherein the object is or relates to genomic fragments immobilized on an array (i.e., the object is related to genomic fragments (e.g., polynucleotides) immobilized on an array, ¶0005).
With respect to claim 5, Trintchouk in view of Price in view of Price the method of claim 1, wherein the detection apparatus includes at least one camera (e.g., the detection apparatus has a least a camera, claim 4).
With respect to claim 6, Trintchouk in view of Price teaches the method of claim 1, wherein the parameter data relates to at least one of a grid orientation angle, an apparent pitch in pixel units, and a phase of a feature grid at a fixed pixel location of the image (e.g., after partitioning the image into a registration image, the image can be analyzed to determine an underlying repeating pattern of features and quantify parameters such as the grid orientation angle, the apparent pitch in pixel units, and the phase of the feature grid at some fixed pixel location, ¶0020).
With respect to claim 7, Trintchouk in view of Price teaches the method of claim 1, wherein quantifying the signal level of each feature comprises building a model of the subimage incorporating known feature locations and corresponding unknown intensities and fitting the model to the image of the object (e.g., wherein quantifying the signal level of each feature comprises building a model of the subimage incorporating known feature locations and corresponding unknown intensities and fitting the model to the image of the object, ¶0058, claim 6).
With respect to claim 8, Trintchouk in view of Price teaches the method of claim 7 wherein the model of the subimage comprises a matrix that is pre-computed and stored in computer memory or a computer-readable medium (e.g., the model of the subimage involves a matrix that is pre-computed and stored in a memory, ¶0020, claim 7).
With respect to claim 9, Trintchouk in view of Price teaches the method of claim 8, wherein the matrix is reused for a different subimage (i.e., matrix is reused for different subimage, ¶0059, claim 8).
With respect to claim 10, Trintchouk in view of Price teaches the method of claim 1, wherein each index address is a unique address (e.g., each index address contains a unique address, ¶0020, claim 9).
With respect to claim 11, Trintchouk in view of Price teaches the method of claim 10, wherein each unique address is an integer vector of length 2 (e.g., refer to claim 10).
With respect to claim 12, Trintchouk in view of Price teaches the method of claim 1, further comprising performing a chromatic correction of the image or image-related data (i.e., performing a chromatic correction of the image or image-related data, ¶0069, claim 11).
With respect to claim 13, Trintchouk in view of Price teaches the method of claim 1, wherein the detection apparatus comprises at least two cameras including a first camera and a second camera and wherein each of the first camera and the second camera is configured to obtain an image of two different color channels (e.g., refer to ¶0069 for details).
With respect to claim 14, Trintchouk in view of Price teaches the method of claim 13, wherein each color channel coincides with a different label used to distinguish one nucleotide base type from another nucleotide base type (e.g., the methods described herein can be used in conjunction with a variety of nucleic acid sequencing techniques. Particularly applicable techniques are those wherein nucleic acids are attached at fixed locations in an array such that their relative positions do not change and wherein the array is repeatedly imaged. Embodiments in which images are obtained in different color channels, for example, coinciding with different labels used to distinguish one nucleotide base type from another are particularly applicable. In some embodiments, the process to determine the nucleotide sequence of a target nucleic acid can be an automated process, ¶0054).
With respect to claim 15, Trintchouk in view of Price teaches the method of claim 13, wherein the first camera collects an image of first and second fluorescent channels and the second camera collects an image of third and fourth fluorescent channels (e.g., wherein the first camera collects an image of first and second fluorescent channels and the second camera collects an image of third and fourth fluorescent channels, claim 14).
With respect to claim 16, Trintchouk in view of Price teaches the method of claim 15, further comprising performing a chromatic correction in order to associate feature images in the channels of a common camera (e.g., performing a chromatic correction in order to associate feature images in the channels of a camera, ¶0069, claim 15).
With respect to claim 17, arguments analogous to claim 1 are applicable. The use of a non-transitory computer-readable medium executed (or performed) by at least a processor (CPU) as described in claim 17 is explicitly taught by ¶0104 of Trintchouk.
With respect to claim 18, this is a system claim corresponding to the apparatus claim 1. Therefore, this is rejected for the same reasons as the apparatus claim 1.
Claims 19 - 24 are rejected under 35 U.S.C. 103 as being unpatentable over Trintchouk in view of Price and further in view of Rotscholl et al. (U.S PreGrant Publication No. 2023/0281758 A1, previously cited in the Office Action dated 09/25/2025, hereinafter ‘Rotscholl’).
With respect to claim 19, Trintchouk in view of Price teaches the system of claim 18, the operations further comprising: forming a first image having substantially same dimensions as the camera image, the first image related to three spatial frequencies (e.g., Since a correction process is performed, there must be an erroneous/degraded/aberrated image formed having substantially same dimension as the camera image (input), the erroneous/degraded/aberrated image is associated to three spatial frequencies, ¶0055 - ¶0056, ¶0069, ¶0077), but fails to teach that said first image is specifically the corrugated image.
However, the mentioned claimed limitation is well-known in the art as evidenced by Rotscholl. In particular, Rotscholl teaches a corrugated image having substantially same dimensions as said camera image (e.g., a moiré interference is formed from camera images, the moiré is associated with (to) spatial frequencies, ¶0027, ¶0048, ¶0181 - ¶0182).
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention was made to modify the system of Trintchouk in view of Price as taught by Rotscholl since Rotscholl suggested within ¶0027, ¶0048 and/or ¶0181 - ¶0182 that such modification would Improve method(s) for suppressing aliasing errors in a Moiré interference in order to obtain greater robustness or greater quality.
With respect to claim 20, Trintchouk in view of Price and further in view of Rotscholl teaches the system of claim 19, wherein the three spatial frequencies describe a hex pattern (e.g., wherein the three spatial frequency describe a hex pattern, ¶0077, ¶0082, Fig. 4A).
With respect to claim 21, Trintchouk in view of Price and further in view of Rotscholl teaches the system of claim 19, wherein the three spatial frequencies relate to vectors each separated by 120 degrees (e.g., the three spatial frequencies are related to vectors each separated by 120 degrees, Fig. 4A with ¶0075 - ¶0077).
With respect to claim 22, Trintchouk in view of Price and further in view of Rotscholl teaches the system of claim 19, wherein Rotscholl further teaches comprising correlating the camera image with the corrugation image to define a complex correlation image (e.g., associating the camera image with the moiré interference to generate a Moiré-corrected result image, ¶0051, ¶0181 - ¶0182).
With respect to claim 23, Trintchouk in view of Price and further in view of Rotscholl teaches the system of claim 22, further comprising calculating a wrapped phase difference to a phase difference image (e.g., phases of a pattern are computed (e.g. calculated) for a geometric center of an overlap region. If the phases derived from the two subimages agree to within a given tolerance (e.g., 0.03 of one feature period by default), the two registrations are deemed in agreement. If there is an inconsistency that has to be resolved, this occurs by revising the registration within one or both of the subimages. The pairwise relationships connect all of the subimages together, so the inconsistencies cannot be resolved by just considering each pair in isolation, ¶0038, ¶0079 - ¶0080).
With respect to claim 24, Trintchouk in view of Price and further in view of Rotscholl teaches the system of claim 23, further comprising unwrapping the phase difference image (e.g., edges where the phase difference exceeds the tolerance were removed (unwrapped), ¶0080).
Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Trintchouk in view of Price and Rotscholl and further in view of Madsen et al. (U.S Patent No. 5,659,318, hereinafter ‘Madsen’).
With respect to claim 25, Trintchouk in view of Price and further in view of Rotscholl teaches the system of claim 24, but neither of them teaches wherein areas having low correlation are not unmasked.
However, in the same field of endeavor of phase unwrapping, Madsen teaches wherein areas having low correlation are not unmasked (Madsen: e.g. wherein regions having low-correlation are filtered (single-out), Col 9 (lines 59 – 67) and Col 10 (lines 11 – 27)).
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention was made to modify the system of Trintchouk in view of Price and Rotscholl as taught by Madsen since Madsen suggested around Col 9 (lines 59 – 67) and Col 10 (lines 11 – 27) that such modification would substantially improves fidelity and efficiency of phase unwrapping by incorporating phase-bootstrapping process in order to achieve good image resolution, which increases/improves complexity in images.
Claims 26 - 29 are rejected under 35 U.S.C. 103 as being unpatentable over Trintchouk in view of Price and Rotscholl, and further in view of Thompson et al. (U.S PreGrant Publication No. 2017/0170917 A1, hereinafter ‘Thompson’).
With respect to claim 26, Trintchouk in view of Price and further in view of Rotscholl teaches the system of claim 24, but neither of them teaches further comprising fitting the phase difference image to a polynomial.
However, in the same field of endeavor of polynomial process, Thompson teaches: further comprising fitting the phase difference image to a polynomial (Thompson: e.g., fitting a unwrapped complex phase difference to a polynomial, ¶0048).
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention was made to modify the system of Trintchouk in view of Rotscholl as taught by Thompson since Thompson suggested in ¶0029 and ¶0048 that such modification would solve differential equations in physics and engineering, particularly those involving spherical symmetry, such as the Schrödinger equation for atoms and Laplace's equation in electrostatics in order to obtain the most approximate/precise result(s) possible.
With respect to claim 27, the integration of Trintchouk, Price, Rotscholl and Thompson teaches the system of claim 26, wherein Thompson teaches the polynomial is a Legendre polynomial (e.g., said polynomial is a Legendre polynomial, ¶0048).
With respect to claim 28, the integration of Trintchouk, Price, Rotscholl and Thompson teaches the system of claim 27, further comprising computing grid locations that correspond to features in the phase difference image (e.g., computing grid coordinates that corresponds to features of the phase difference , ¶0080).
With respect to claim 29, the integration of Trintchouk, Price, Rotscholl and Thompson teaches the system of claim 28, further comprising deconvoluting optical blurring of the image (e.g., deconvoluting a distorted portion of the image, ¶0049, ¶0061).
Conclusion
The prior art made of record and not relied upon are considered pertinent to applicant's disclosure:
Othmezouri et al. (U.S PG Publication No. 2016/0117571 A1)1
Yaqub et al. (U.S PG Publication No. 2019/0385307 A1)2
1This reference teaches receiving a plurality of images from a camera, many of the plurality of images are similar and different intensity or color values; dividing the image(s) into cells of pixels, and choosing a detection window within the image(s), and a self similarity computation part (40) for determining self-similarity information for a group of the pixels in any part of the detection window, to represent an amount of self-similarity of that group to other groups in any other part of the detector window, and for repeating the determination for groups in all parts of the detection window, to generate a global self similarity descriptor for the detection window. Then, a classifier (50) is used for classifying whether an object is present based on the global self-similarity descriptor. By using global self-similarity rather than local similarities more information is captured which can lead to better classification. In particular, it helps enable recognition of more distant self-similarities inherent in the object, and self-similarities present at any scale.
2This reference teaches obtaining images with similar appearance; partitioning said image into blocks; detects the one or more structures within said images based on the computed correlation; and categorizes (assigns by labeling) biological or medical images by the one or more structures detected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JUAN M GUILLERMETY whose telephone number is (571)270-3481. The examiner can normally be reached 9:00AM - 5:00PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Benny Q TIEU can be reached at 571-272-7490. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JUAN M GUILLERMETY/Primary Examiner, Art Unit 2682