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 Status Original claims 1-30 are currently pending. Priority This application filed 9/14/2022 claims benefit to US Provisional application 63/247296 and 63/247301 both filed on 9/27/2021; and to 17/944809 through claim of benefit to the provisional applications now US Patent 12,412387. Information Disclosure Statement The four information disclosure statements (IDS) submitted on 1/12/2023 through 5/8/2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner. The listing of references in the specification is not a proper information disclosure statement. See for example the section labelled Incorporations, and compared to IDS filed. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered. Double Patenting The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg , 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman , 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi , 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum , 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel , 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington , 418 F.2d 528, 163 USPQ 644 (CCPA 1969). A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA. A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b). The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13. The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA/25, or PTO/AIA/26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer . Claims 1-30 are rejected on the ground of nonstatutory double patenting a s being unpatentable over the claims of U.S. Patent No. 12,412387 (US Application 17/944809 ) . Although the claims at issue are not identical, they are not patentably distinct from each other because while the present claims are slightly broader, each provide a system and method implemented on the system that analyzes images of clusters , including images of sequencing. A copy of claim 1 and 4 from ‘387 is provided for comparison to the instantly pending claims: Claim 1 A system, comprising: memory storing, for a current sequencing cycle of a sequencing run, respective current intensity values for respective pixels in a plurality of pixels; the memory storing, for one or more previous sequencing cycles of the sequencing run that precede the current sequencing cycle, sequences of respective previous intensity values for the respective pixels; a state generator, having access to the memory, configured to generate respective current state values for the respective pixels in dependence upon ( i ) the respective current intensity values, and (ii) respective previous intensity values in the sequences of respective previous intensity values, and to store the respective current state values in the memory; and a base caller, having access to the memory, configured to generate base calls for the current sequencing cycle in response to processing ( i ) the respective current intensity values, and (ii) the respective current state values. Claim 4 The system of claim 3, wherein the respective current state values are pixel-wise encoded with the respective current intensity values. Claim Interpretation The following is a quotation of 35 U.S.C. 112(f): (f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph: An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked. As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph: (A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function; (B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and (C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function. Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function. Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function. Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) the various system components such as spatial convolution neural network, filtering logic, compression logic; which in view of the specification appear to be programs or code such as a series of instructions which are performed on a computer system. Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. 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 appl icant regards as his invention. Claims 1-30 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. Specifically, the claim provides for a system and a list of elements that are ‘configured’ to provide a general outcome but is broadly applied to any ‘images of clusters’. The claim appears to be a listing of general components or general instructions with no clear link as how or what they specifically perform for any given image of ‘sequencing images of clusters’ , and for a final step for any image a ‘base calling logic’ which can ‘generate base calls’. More clearly providing the nature of the data and steps which the various limitations provide would address the basis of the rejection. Claim Rejections - 35 USC § 101 35 U.S.C. 101 reads as follows: Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title. Claims 1- 30 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. Claim analysis Claim 1 is generally directed to a system which uses a neural network, logic to identify features, logic to compress features, contextual logic to provide ‘stateful compressed features and another neural network which can provide base calling from the process performed on the image. In view of the specification, the process is intended on obtaining ‘pixel’ information that may be in the image and based on common sequencing features like different fluorescent molecules ( ie channel by channel, intensity,…) for each of the bases, evaluates the information to ‘cluster’ pixel as a features which can differentiate each of the bases. The claims are broad to any image, but appear to be consistent with fluorescent data produced during a sequencing reaction or during the resolution on a column or gel . Dependent claims provide for additional details for the analysis performed at each of the steps of claim 1. It is noted that the claims are directed to a system, however it appears that the system can be a series of instructions or instructions performed on a system such as a computer. For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a product . For step 2A of the 101 analysis, the judicial exception of the claims are the steps of assessing sequence data which is provided in the basis of an image and interpreting the image as to what bases are represented . The step of assessing bits of channel data for features such as color of fluorophore to correlate to sequence reads are considered instructional steps. The claim requires assessing sequencing data that is provided as an image and correlating the image data to sequence data or base calling . The judicial exception is a set of instructions for analysis of sequence image data and broadly provides for visually inspecting an image of a gel or an image of fluorophore color images of a sequence processes and appears to gall into the category of Mental Processes , that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) here interpreting a gel image with four different color representing each of the four bases of a sequence; and also Mathematical Concepts such as mathematical relationships or mathematical formulas or equations as the claims may require data of intensity which can then be mathematically analyzed for example for area under a curve. No specific image is required, nor any specific means of clustering, compression or contextualization in evaluating the image which represents the sequence created over time as a temporal feature of the image. The breadth o f each of the ‘configured’ elements encompasses non-transformative visual assessment of an image, which may be coupled with prior knowledge of the correlation of said data image or feature and what it represents . This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle of oabserving an image of a sequence gel and interpreting the bases based on their profile and color . Although the claims recite the use of a neural network and various general forms of logic, the courts have also identified limitations that did not integrate a judicial exception into a practical application; for example, merely including instructions to implement an abstract idea on a computer i.e. ‘neural network’ , or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f). The recited breeding crosses are interpreted as naturally occurring plant crosses. Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. See MPEP § 2106.05(g) for a discussion on adding insignificant extra-solution (both pre-solution and post-solution) activity to the judicial exception. See also MPEP § 2106.05(h) for a discussion on generally linking the use of a judicial exception to a particular technological environment or field of use. The claims appear to fall into the category of Mathematical Concepts, as it applies the use of statistics and mathematical relationships in analyzing ‘coefficients’ broadly that might be present or represented in the image , and also into the category of mental processes, as concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because there is no apparent complexity to or amount of data that is collected and analyzed as presently claimed. Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element to which the analysis is applied. The claims generically provide for an image and steps of analysis which when performed provide for what the image represents relative to a sequence . This judicial exception requires steps recited at high level of generality and if or when implemented on a computer are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth. For step 2B of the 101 analysis, each of the independent claims recites additional elements and are found to be the steps of obtaining an image representing sequence data. As such, the claims do not provide for any additional element to consider under step 2B beyond a computer which implements instructions to evaluate an image. To the extent the analysis of the image is performed with a system or on a computer, it is noted that in e xplaining the Alice framework, the Court wrote that "[ i ]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s] ince Alice , we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of sequence data presented in the form of an image . While the instruction can be stored on a medium and could be implemented on a computer, together the steps do not appear to result in significantly more than a means to analyze data of sequences. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis. As such, the instant claims set forth an inventive concept that are drawn only to an abstract process that only manipulates data and, therefore, are not directed to statutory subject matter. Therefore the result of Step 2A analysis is that the claims are directed towards a judicial exception, i.e. an abstract idea. The second part, Step 2B of the two step analysis is to determine whether any element or combination of elements, in the claim is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception. Without additional limitations, a process that employs mathematical algorithms ( assessing images of sequences) to manipulate existing information (identify a correlation of the bases represented ) to generate additional information is not patent eligible. Furthermore, if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is non-statutory. In other words, patenting abstract idea (designing probes to a target sequence) cannot be circumvented by attempting to limit the use to a particular technological environment or purpose and desired result. One way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments. Conclusion No claim is allowed The closest art of record is prior art US PgPub No. 2015/0169824 by Kermani et al. (hereinafter ' Kermani ') which teaches a system, comprising: memory storing current sequencing images for clusters for a current sequencing cycle of a sequencing run, and previous sequencing images for the clusters for one or more previous sequencing cycles of the sequencing run that precede the current sequencing cycle; (See Kermani Figure 1, element 20 & 21 and paragraph [0042], Kermani teaches data repository comprising images of sequencing cycles.) a configurable processor having access to the memory and configured to execute a neural network to produce base call classification scores; and (See Kermani paragraph [0184], Kermani teaches neural network for producing confidence scores.) a data flow logic having access to the memory, the host processor, and the configurable processor and configured to provide the current per pixel states and the current sequencing images to the neural network and cause the neural network to produce current base call classification scores for the clusters for the current sequencing cycle in response to processing the current per-pixel states and the current sequencing images, and to provide the current base call classification scores to the host. (See Kermani paragraphs [0186]-[0189], Kermani teaches confidence scores using neural network.) However, Kerman does not teach or suggest the specific limitations required of the claims. Any inquiry concerning this communication or earlier communications from the examiner should be directed to FILLIN "Examiner name" \* MERGEFORMAT Joseph T Woitach whose telephone number is FILLIN "Phone number" \* MERGEFORMAT (571)272-0739 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT Mon-Fri; 8:00-4:00 . 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. 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If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /Joseph Woitach/ Primary Examiner, Art Unit 1687