DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s election without traverse of Group II, directed to claims 18-31, 45, 48-50, and 53, in the reply filed on 18 February 2026 is acknowledged.
Claims 1-57 are all the claims pending in the application, of which claims 1-17, 32-44, 46-47, 51-52, and 54-57 are withdrawn. Claims 18-26, 45, and 50 are rejected. Claims 27-31, 48-49 and 53 are objected to.
Claim Objections
Claim 53 is objected to under 37 CFR 1.75(c) as being in improper form because a multiple dependent claim should refer to other claims in the alternative only, whereas claim 53 refers to both claim 25 and claim 1. See MPEP § 608.01(n). Accordingly, the claim has not been further treated on the merits.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 20-24 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 20 recites “the signal portion function”. Although this limitation is recited in claim 19, claim 20 is directly dependent on claim 18. Accordingly, the limitation lacks antecedent basis.
Claim 21 recites “the optimization”. Although claim 19 recites “optimizing the signal portion” is recited in claim 19, claim 21 is directly dependent on claim 18. Accordingly, the limitation lacks antecedent basis.
Claims 22-24 inherit the deficiencies of their parent claim 21.
Additionally, claim 22 recites the phrase "for example" which renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claims 23-24 inherit the deficiencies of their parent claim 22.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 18-22 and 50 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by U.S. Patent Application Publication No. 2024/0428880 to Marks et al. (hereinafter “Marks”).
As to independent claim 18, Marks discloses a method for determining a signal composition of signal series of an image series with an analyte data evaluation system, wherein the image series is generated by marking analytes with markers in a plurality of coloring rounds and detecting the markers with a camera, wherein the camera acquires an image of the image series in each coloring round, the markers are selected in such a way that the signal series of analytes in an image area across the image series comprise colored and uncolored signals and the signal series of different analyte types each have a specific sequence of colored signals and uncolored signals, and the different analyte types can be identified from the specific sequences (Abstract and [0089, 0127-0136, 0171] discloses that Marks is directed to a system for “identifying…one or more barcoded target analytes” by “receiving images of a biological sample acquired during a cyclical decoding process; detecting a series of detectable signals (ON signals) or absence thereof (OFF signals) at one or more locations in the biological sample corresponding to one or more barcoded target analytes; determining a code word based on the series of ON and OFF signals that corresponds to a barcode for each of the one or more barcoded target analytes”, wherein the image series may be generated “using sequential rounds of fluorescent hybridization” in which “Microscopy may be used to analyze 4 or 5 fluorescent colors indicative of the spatial localization of a target, followed by various rounds of hybridization and stripping, in order to generate a large set of unique optical signal signatures assigned to different analytes” resulting in “a string of signals associated with each target analyte”), comprising: - receiving signal series, - importing a codebook, wherein the codebook comprises a target series for all signal components, the target series comprise analyte target series, and the analyte target series comprise a sequence of true and false values according to the specific sequences of the signal series of the different analyte types, and - determining the signal composition for each of the signal series, wherein the signal components are assigned a signal portion in the respective signal series according to the signal composition ([0019-0024, 0136-0155] discloses receiving the detected “series of ON and OFF bits” (which reads on the claimed true and false values), and identifying corresponding “unique code words…assigned to the unique target analytes” from a “codebook” ).
As to claim 19, Marks further discloses that the signal composition is determined on the basis of a signal portion function, wherein the signal portion function detects a difference between the signal series and a linear combination of a plurality of the target series, and the signal composition determination further comprises: - optimizing the signal portion function based on the signal portions ([0014-0025, 0151-0161] discloses using a “simulated annealing algorithm” for achieving “optimized assignment of code words to target analytes”, wherein such an optimization is necessarily performed using a function subject to “minimiz[ation]” of “the predicted density of ON signals across the series of images” in order to decode “every combination of remaining, unassigned code words and the barcoded target analyte”).
As to claim 20, Marks further discloses that the signal portion function is optimized by using at least one of the following algorithms: a classical optimization algorithm, a non-negative matrix factorization, a main component analysis, a discriminant function, or a singular value decomposition ([0014-0025, 0151-0161] discloses using a “simulated annealing algorithm” for achieving “optimized assignment of code words to target analytes”, wherein simulated annealing is a classical optimization algorithm).
As to claim 21, Marks further discloses that the optimization is performed based on predetermined constraints ([0014-0025, 0151-0161] discloses a “decision rule” upon which the minimization/optimization algorithm for code word assignment is based).
As to claim 22, Marks further discloses that the constraints comprise at least one of the following: - the values of the signal portions can be non-negative, - the entries in the target series can be non-negative, - the number of the colored signals in a target series is predetermined for all analyte types in the codebook, for example as a fixed value or as an interval, - the number of the colored signals is specified individually for each of the nominal sequences ([0089, 0141] disclose that ON bits are assigned numeric value of “1” in the signal and OFF bits are assigned “0”, both of which are non-negative).
As to claim 50, Marks further discloses the receiving of signal series comprises at least one of the following: - extracting all image areas of the image series, - extracting a random selection of the image areas of the image series, - extracting a selection of the image areas of the image series weighted with a structural property of the image areas, for example, with a higher probability for cells, cell nuclei, and bright pixels, - extracting image areas exclusively from image areas with a minimum degree of image sharpness, and - skipping image areas in which no analytes are to be expected (the claimed alternatives are interpreted in the disjunctive; [0035] discloses “detecting, in the images of the series of images, a series of detectable signals (ON signals) or absence thereof (OFF signals) at one or more locations in the biological sample corresponding to one or more barcoded target analytes”, wherein the detections at the one or more locations require extraction of those particular image areas while skipping other locations that don’t correspond to the analytes).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 23-24 are rejected under 35 U.S.C. 103 as being unpatentable over Marks in view of U.S. Patent Application Publication No. 2024/0257912 to Deisseroth et al. (hereinafter “Deisseroth”).
As to claim 23, Marks does not expressly disclose that the optimization is performed with regularizations.
Deisseroth, like Marks, is directed to “iteratively matching signals across rounds of sequencing to membership in the codebook”, wherein the signal is acquired from “sequential analysis of images” displaying a “fluorescent signal” over the multiple rounds (Abstract and [0003, 0056-0074]). Deisseroth discloses that the signal decoding is performed using “posterior likelihood probabilities with regularization or sparsity constraints”, for example, by using a “sparse dictionary of known codes” ([0067, 0330]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Marks to perform the optimization of code assignment using sparse solutions as a regularization, as taught by Deisseroth, to arrive at the claimed invention discussed above. Such a modification is the result of combining prior art elements according to known methods to yield predictable results. It is predictable that the proposed modification would have reduced overfitting and saved computational overhead by virtue of generating a simpler, more focused model.
As to claim 24, Marks as modified above further teaches that the regularizations comprise at least one of the following: - a predetermined maximum number of distinct signal components, - an expected number of analyte types, - a limitation of the combinability of the analyte types with each other, - a limitation of the optimization to sparse solutions ([0067, 0330] of Deisseroth discloses that the signal decoding is performed using “posterior likelihood probabilities with regularization or sparsity constraints”, for example, by using a “sparse dictionary of known codes”; the reasons for combining the references are the same as those discussed above in conjunction with claim 23).
Claims 25-26 are rejected under 35 U.S.C. 103 as being unpatentable over Marks in view of U.S. Patent Application Publication No. 2023/0026084 to Kia et al. (hereinafter “Kia”).
As to claim 25, Marks does not expressly disclose that the determination of a signal composition comprises: - inputting the signal series into a processing model, wherein the processing model was trained to provide a result output from which the signal portion to the respective signal series is determined for each signal component.
Kia, like Marks, is directed to analyzing an analyte in a spatially aligned position across multiple images (Abstract, Fig. 8B). In particular, Kia discloses a neural network trained to input data for the spatially aligned patches and output a classification of the analytes therein ([0122-0147]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Marks to use a neural network to classify the signal, as taught by Kia, to arrive at the claimed invention discussed above. Such a modification is the result of combining prior art elements according to known methods to yield predictable results. It is predictable that the proposed modification would have enhanced the accuracy of the classification result.
As to claim 26, Marks as modified above further teaches that the processing model is a classification model, the result output for each signal series is a probability distribution across the signal components to be identified, each indicating a probability of belonging to one of the signal components to be identified, and the signal portion is determined on the basis of the probability distribution ([0122-0147] of Kia discloses a neural network trained to input data for the spatially aligned patches and output probabilities of various classifications of the analytes therein using a softmax function; the reasons for combining the references are the same as those discussed above in conjunction with claim 25).
Claim 45 is rejected under 35 U.S.C. 103 as being unpatentable over Marks in view of U.S. Patent Application Publication No. 2021/0279866 to Svekolkin et al. (hereinafter “Svekolkin”).
As to claim 45, Marks discloses that the barcoded target analytes are extracted from “clustered cell types” found in the biological sample ([0153-0154]) but does not expressly disclose that the determination of a signal composition comprises non-maximum suppression.
Svekolkin, like Marks, is directed to segmenting cells in images for analysis (Abstract). Svekolkin discloses that the segmentation process uses the “non-maximum suppression algorithm” ([0267]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Marks to use non-maximum suppression for segmenting/clustering the cells from which the signal is extracted, as taught by Svekolkin, to arrive at the claimed invention discussed above. Such a modification is the result of combining prior art elements according to known methods to yield predictable results. It is predictable that the proposed modification would have reduced redundancy in the segmentation results.
Allowable Subject Matter
Claims 27-31 and 48-49 are 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.
Pertinent Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Kuhnemund (U.S. Patent Application Publication No. 2023/0012607) is directed to reducing the crowding of signals in the detection of barcode sequences of multiple target nucleic acid sequences in a sample using hybridization probes.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SEAN M CONNER whose telephone number is (571)272-1486. The examiner can normally be reached 10 AM - 6 PM Monday through Friday, and some Saturday afternoons.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Greg Morse can be reached at (571) 272-3838. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/SEAN M CONNER/Primary Examiner, Art Unit 2663
Prosecution Insights