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 .
1. Acknowledgement is made to the preliminary amendment, filed 5/30/2025. Claims 1-20 are pending.
Priority
2. The instant application claims benefit of US Provisional Application No. 63/552,608, filed 2/12/2024.
Information Disclosure Statement
3. Acknowledgement is made to the information disclosure statement (IDS) submitted on 7/15/2025. The information disclosure statement is being considered by the examiner.
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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
4. Claims 1-3, 6-8, & 20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Shah (US 2022/0083832 A1).
Regarding claim 1, Shah discloses a computer-implemented method to assign barcodes from images of dots representing fluorescent probes interacting with molecular targets, to a plurality of molecular targets, the method comprising:
(i) using a computer, tracing dots between images within a search radius (r) and assigning dots to barcodes to form a plurality of candidate barcodes [0013, 0028, 0121, 0123, & 0126 – disclosing obtaining an image for each decoding cycle of a plurality of decoding cycles to obtain a series of images for a given field-of-view… detecting, in each image… one or more locations of one or more respective barcode probe sequences… and the identifying and selecting of candidate barcodes];
(ii) using a computer, assigning a cost to the plurality of candidate barcodes to obtain an assigned cost [0237-0239 – disclosing the calculating of a negative log likelihood for candidate barcodes and thus the selecting of candidate barcodes based on trying to minimize this would be equivalent to reducing a cost or energy function in terms of computer processing and/or optimization];
(iii) using a computer, for the plurality of candidate barcodes, assigning a penalty to unused dots in each of the images to obtain a penalty cost [0210, 0211, & 0237-0239];
(iv) using a computer, choosing a trial solution, the trial solution comprising a set of candidate barcodes with the smallest cost [0237-0239]; and
(v) using a computer, assigning the candidate barcodes, selected by the trial solution, with the smallest cost to the molecular targets [0010, 0011, 0237-0239, 0258-0260, & Fig. 27].
Regarding claim 2, Shah discloses the method of claim 1, further comprising for each candidate barcode in the plurality of candidate barcodes, adding the assigned cost to the penalty cost [0210].
Regarding claim 3, Shah discloses the method of claim 1, further comprising summing the assigned cost and the penalty cost for each of the plurality of candidate barcodes to obtain a respective total cost [0210].
Regarding claim 6, Shah discloses the method of claim 1, further comprising aligning each of the images using one or more reference positions in each image [0010 & 0275].
Regarding claim 7, Shah discloses the method of claim 1, wherein candidate barcodes are selected from linear codes [0012 & 0121-0123].
Regarding claim 8, Shah discloses the method of claim 7, wherein the linear codes are selected from the group consisting of BCH codes and Hamming codes [0010, 0011, 0112, & 0121-0123].
Regarding claim 20, Shah discloses the method of claim 1, where spatial positions of the candidate barcodes can be determined by taking mean, median, or other functions, of the spatial positions of the dots that make up the candidate barcodes [0210].
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.
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.
5. Claims 4, 5, & 9-19 are rejected under 35 U.S.C. 103 as being unpatentable over Shah in view of Cai et al. (WO 2018/026873 A1), hereinafter Cai.
With respect to claims 4 & 5, the teachings of Shah have been discussed above.
Shah is silent with respect to explicitly disclosing wherein the dots in each of the images are fitted to a function that determines their spatial coordinates, as recited in claim 4, and wherein the function is Gaussian or Airy, as recited in claim 5.
Cai teaches, regarding claims 4 & 5, wherein the dots in each of the images are fitted to a function that determines their spatial coordinates, wherein the function is Gaussian or Airy [0231, 0257, & 0267].
It would have been obvious to one of ordinary skill in the art at the time the invention was made to further employ the fitting function features of Cai within the system and method of Shah for at least the benefit of providing for better resolved image data with more focus and a higher resolution [0231, 0257, & 0267].
With respect to claims 10 & 11, the teachings of Shah have been discussed above.
Shah is silent with respect to explicitly disclosing further comprising assigning each dot a pseudo-color value or symbol in each image, as recited in claim 10, and wherein the symbol is an element of a codeword, wherein the codeword identifies the molecular target, as recited in claim 11.
Cai teaches, regarding claims 10 & 11, further comprising assigning each dot a pseudo-color value or symbol in each image [0205, 0209, & 0223], wherein the symbol is an element of a codeword, wherein the codeword identifies the molecular target [0036, 0041, 0049, & 0050].
It would have been obvious to one of ordinary skill in the art at the time the invention was made to further employ the pseudo-color features of Cai within the system and method of Shah for at least the benefit of improving imaging efficiency and decreasing imaging time [0209].
With respect to claim 9, the teachings of Shah have been discussed above.
Shah is silent with respect to explicitly disclosing wherein the linear code is a Reed-Solomon code, as recited in claim 9.
Cai is also silent with respect to explicitly disclosing the term “Reed-Solomon code”.
However, both Shah and Cai discuss error correcting codes such as Hamming codes and Golay codes. One of ordinary skill in the art would recognize that merely substituting a known linear error-correcting code with another, such as Reed-Solomon, which is known for being highly efficient for use in burst error correction and for multiple-bit errors, would have been an obvious matter of design choice based upon the intended use and/or specifics of the environment of use.
Regarding claim 12, Cai, as modified above, discloses the method of claim 1, comprising identifying each candidate barcode using a coding scheme that does not have parity checks [0406].
Regarding claim 13, Shah, as modified above, discloses the method of claim 1, further comprising resolving conflicting candidate barcodes that use at least one of the same dots [0122, & 0123, & 0151-0153].
Regarding claim 14, Shah, as modified above, discloses the method of claim 1, further comprising identifying candidate barcodes by summing syndromes [0122, & 0123, & 0151-0153].
Regarding claim 15, Shah, as modified above, discloses the method of claim 1, wherein the cost is an error function measuring the deviation of the observed pixel intensities from the pixel intensities predicted by trial solutions and is determined according to: C = f(Nnd) wherein Nnd is a number of dots in the images that are not used in the candidate barcodes, and f is a function [0210, 0211, & 0237-0239].
Regarding claim 16, Shah, as modified above, discloses the method of claim 1, wherein the cost is determined according to:
C =
∑
b
B
(
a
1
v
a
r
x
b
+
v
a
r
y
b
+
a
2
v
a
r
log
I
b
+
a
3
δ
i
m
p
e
r
f
e
c
t
(
b
)
)
+
N
n
d
where B is the set of all barcode candidates in the trial solution, b is a barcode candidate in B, and var (xb), var (yb), and var (log(Ib)) are the variances of x-coordinates; y-coordinates and log intensities of each dot in the candidate barcode b;
δ
i
m
p
e
r
f
e
c
t
is an indicator variable that is equal to 1 when b is an imperfect barcode and equal to 0 when it is a perfect barcode; a3 is a position variance penalty; a2 is a weight variance penalty; a3 is a penalty for imperfect barcodes, are user set parameters; Nnd is a number of dots in the images that are not used in the candidate barcodes [0160-0165 & 0210-0220]
Regarding claim 17, Shah, as modified above, discloses the method of claim 13, further comprising using dynamic programming to identify codepaths, wherein the codepaths are candidate barcodes [0010, 0011, & 0121-0123].
Regarding claim 18, Cai, as modified above, discloses the method of claim 1, wherein the cost is determined using pixel intensities in the images and deviations from the pixel intensities predicted by the trial solutions [0257 & 0267-0269].
Regarding claim 19, Shah, as modified above, discloses the method of claim 1, wherein the cost is determined using regularized regression to select candidate barcodes that account for dots in images [0144 & 0160-0165].
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PAULTEP SAVUSDIPHOL whose telephone number is (571)270-1301. The examiner can normally be reached on M-F,7-3 EST. If the examiner cannot be reached by telephone, he can be reached through the following email address: paultep.savusdiphol@uspto.gov
If attempts to reach the examiner by telephone and email are unsuccessful, the examiner’s supervisor, Michael G. Lee can be reached on (571) 272-2398. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PAULTEP SAVUSDIPHOL/Primary Examiner, Art Unit 2876