Prosecution Insights
Last updated: July 17, 2026
Application No. 18/943,587

Strategy and technological implementations for concurrent fluorescence measurements of multiple biological parameters in behaving animals

Non-Final OA §101
Filed
Nov 11, 2024
Priority
Jun 20, 2023 — provisional 63/522,044 +2 more
Examiner
VARGAS, DIXOMARA
Art Unit
Tech Center
Assignee
Howard Hughes Medical Institute
OA Round
1 (Non-Final)
93%
Grant Probability
Favorable
1-2
OA Rounds
12m
Est. Remaining
99%
With Interview

Examiner Intelligence

Grants 93% — above average
93%
Career Allowance Rate
936 granted / 1011 resolved
+32.6% vs TC avg
Moderate +8% lift
Without
With
+8.4%
Interview Lift
resolved cases with interview
Typical timeline
2y 8m
Avg Prosecution
27 currently pending
Career history
1038
Total Applications
across all art units

Statute-Specific Performance

§101
10.7%
-29.3% vs TC avg
§103
39.9%
-0.1% vs TC avg
§102
39.1%
-0.9% vs TC avg
§112
5.4%
-34.6% vs TC avg
Black line = Tech Center average estimate • Based on career data from 1011 resolved cases

Office Action

§101
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 § 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. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action. Claims 1-18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a method without significantly more. The claim(s) recite(s) a method for measuring a parameter by processing the signals to determine values. This judicial exception is not integrated into a practical application because the claim is directed to an abstract idea with additional generic computer elements, where the generically recited computer elements do not add a meaningful limitation to the abstract idea because they amount to simply implementing the abstract idea on a computer. Furthermore, the claim is directed to a method of using a naturally occurring correlation of values or parameters as data gathering steps required to use the correlation where the data gathering and correlation do not add a meaningful limitation to the method as they are insignificant extra-solution activity. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements when considered separately and in combination, they do not add significantly more to the exception. For example, if the additional limitations only store and retrieve information in memory, explain that these are well-understood, routine, conventional computer functions as recognized by the court decisions listed in MPEP § 2106.05(d) Claims 1-18 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. Each of Claims 1-18 has been analyzed to determine whether it is directed to any judicial exceptions. Specifically, Claim 1 recites: 1. A method for concurrently measuring multiple biological parameters in an animal, the method comprising: a) illuminating using multiple illumination sources a region-of-interest of the animal that expresses a first genetically encoded fluorescent indicators (GEFI), a second GEFI, and a long-Stokes-shift (LSS) fluorescent compound that is insensitive to the multiple biological parameters, wherein an absorption spectrum of the first GEFI is distinct from an absorption spectrum of the second GEFI, wherein the illuminating excites the first GEFI, the second GEFI, and the LSS fluorescent compound, wherein an absorption spectrum of the LSS fluorescent compound overlaps the absorption spectrum of the first GEFI, wherein an emission spectrum of the LSS fluorescent compound overlaps with an emission spectrum of the second GEFI; b) concurrently detecting fluorescence signals from the first GEFI, the second GEFI, and the LSS fluorescent compound using a multi-channel fluorescence sensing optical system; c) processing the detected fluorescence signals to determine values of the multiple biological parameters, wherein the processing reduces instrument and/or biological artifacts in the values of the multiple biological parameters. Further, dependent Claims 2-18 merely include limitations that either further define the abstract idea (and thus don’t make the abstract idea any less abstract) or amount to no more than generally linking the use of the abstract idea to a particular technological environment or field of use because they’re merely incidental or token additions to the claims that do not alter or affect how the process steps are performed. The above-identified abstract idea in independent Claim 1 (and their respective dependent Claims 2-18) is not integrated into a practical application under 2019 PEG because the additional elements (identified above in independent Claims 1, either alone or in combination, generally link the use of the above-identified abstract idea to a particular technological environment or field of use. More specifically, the additional elements of: a processor, as recited in independent Claim 1 and its dependent claims; are generically recited computer elements in independent Claim 1 (and their respective dependent claims) which do not improve the functioning of a computer, or any other technology or technical field. Nor do these above-identified additional elements serve to apply the above-identified abstract idea with, or by use of, a particular machine, effect a transformation or apply or use the above-identified abstract idea in some other meaningful way beyond generally linking the use thereof to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. Furthermore, the above-identified additional elements do not add a meaningful limitation to the abstract idea because they amount to simply implementing the abstract idea on a computer. For at least these reasons, the abstract idea identified above in independent Claim 1 (and their respective dependent claims) is not integrated into a practical application under 2019 PEG. Moreover, the above-identified abstract idea is not integrated into a practical application under 2019 PEG because the claimed method and system merely implements the above-identified abstract idea (e.g., mental process and certain method of organizing human activity) using rules (e.g., computer instructions) executed by a computer (e.g., a processor, as claimed). In other words, these claims are merely directed to an abstract idea with additional generic computer elements which do not add a meaningful limitation to the abstract idea because they amount to simply implementing the abstract idea on a computer. Additionally, Applicant’s specification does not include any discussion of how the claimed invention provides a technical improvement realized by these claims over the prior art or any explanation of a technical problem having an unconventional technical solution that is expressed in these claims. That is, like Affinity Labs of Tex. v. DirecTV, LLC, the specification fails to provide sufficient details regarding the manner in which the claimed invention accomplishes any technical improvement or solution. Thus, for these additional reasons, the abstract idea identified above in independent Claim 1 (and their respective dependent claims) is not integrated into a practical application under the 2019 PEG. Accordingly, independent Claim 1 (and their respective dependent claims) are each directed to an abstract idea under 2019 PEG. None of Claims 1-18 include additional elements that are sufficient to amount to significantly more than the abstract idea for at least the following reasons. These claims require the additional elements of: a processor, as recited in independent Claim 1 and its dependent claims. Per Applicant’s specification, according to paragraph 0044 in Applicant’s Specification discusses a processor, in generic terms without structure or detailed drawings, e.g., schematic drawing or described as an iphone or ipad or mobile device or personal computer or laptop. Therefore, the processor is well understood, routine and conventional. Accordingly, in light of Applicant’s specification, the claimed term processor is reasonably construed as a generic computing device. Like SAP America vs Investpic, LLC (Federal Circuit 2018), it is clear, from the claims themselves and the specification, that these limitations require no improved computer resources, just already available computers, with their already available basic functions, to use as tools in executing the claimed process. Furthermore, Applicant’s specification does not describe any special programming or algorithms required for the processor. This lack of disclosure is acceptable under 35 U.S.C. §112(a) since this hardware performs non-specialized functions known by those of ordinary skill in the computer arts. By omitting any specialized programming or algorithms, Applicant's specification essentially admits that this hardware is conventional and performs well understood, routine and conventional activities in the computer industry or arts. In other words, Applicant’s specification demonstrates the well-understood, routine, conventional nature of the above-identified additional elements because it describes these additional elements in a manner that indicates that the additional elements are sufficiently well-known that the specification does not need to describe the particulars of such additional elements to satisfy 35 U.S.C. § 112(a) (see Berkheimer memo from April 19, 2018, (III)(A)(1) on page 3). Adding hardware that performs “‘well understood, routine, conventional activit[ies]’ previously known to the industry” will not make claims patent-eligible (TLI Communications). The recitation of the above-identified additional limitations in Claims 1-18 amounts to mere instructions to implement the abstract idea on a computer. Simply using a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); and TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Moreover, implementing an abstract idea on a generic computer, does not add significantly more, similar to how the recitation of the computer in the claim in Alice amounted to mere instructions to apply the abstract idea of intermediated settlement on a generic computer. A claim that purports to improve computer capabilities or to improve an existing technology may provide significantly more. McRO, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299, 1314-15, 120 USPQ2d 1091, 1101-02 (Fed. Cir. 2016); and Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1335-36, 118 USPQ2d 1684, 1688-89 (Fed. Cir. 2016). However, a technical explanation as to how to implement the invention should be present in the specification for any assertion that the invention improves upon conventional functioning of a computer, or upon conventional technology or technological processes. That is, the disclosure must provide sufficient details such that one of ordinary skill in the art would recognize the claimed invention as providing an improvement. Here, Applicant’s specification does not include any discussion of how the claimed invention provides a technical improvement realized by these claims over the prior art or any explanation of a technical problem having an unconventional technical solution that is expressed in these claims. Instead, as in Affinity Labs of Tex. v. DirecTV, LLC 838 F.3d 1253, 1263-64, 120 USPQ2d 1201, 1207-08 (Fed. Cir. 2016), the specification fails to provide sufficient details regarding the manner in which the claimed invention accomplishes any technical improvement or solution. For at least the above reasons, the method of Claims 1-18 is directed to applying an abstract idea (e.g., mental process or certain method of organizing human activity) on a general-purpose computer without (i) improving the performance of the computer itself (as in McRO, Bascom and Enfish), or (ii) providing a technical solution to a problem in a technical field (as in DDR). In other words, none of Claims 1-18 provide meaningful limitations to transform the abstract idea into a patent eligible application of the abstract idea such that these claims amount to significantly more than the abstract idea itself. Taking the additional elements individually and in combination, the additional elements do not provide significantly more. Specifically, when viewed individually, the above-identified additional elements in independent Claim 1 (and their dependent claims) do not add significantly more because they are simply an attempt to limit the abstract idea to a particular technological environment. That is, neither the general computer elements nor any other additional element adds meaningful limitations to the abstract idea because these additional elements represent insignificant extra-solution activity. When viewed as a combination, these above-identified additional elements simply instruct the practitioner to implement the claimed functions with well-understood, routine and conventional activity specified at a high level of generality in a particular technological environment. As such, there is no inventive concept sufficient to transform the claimed subject matter into a patent-eligible application. As such, the above-identified additional elements, when viewed as whole, do not provide meaningful limitations to transform the abstract idea into a patent eligible application of the abstract idea such that the claims amount to significantly more than the abstract idea itself. Thus, Claims 1-18 merely apply an abstract idea to a computer and do not (i) improve the performance of the computer itself (as in Bascom and Enfish), or (ii) provide a technical solution to a problem in a technical field (as in DDR). Therefore, none of the Claims 1-18 amounts to significantly more than the abstract idea itself. Accordingly, claims 1-18 are not patent eligible and rejected under 35 U.S.C. 101 as being directed to abstract ideas implemented on a generic computer in view of the Supreme Court Decision in Alice Corporation Pty. Ltd. v. CLS Bank International, et al. and 2019 PEG. Allowable Subject Matter The following is an examiner’s statement of reasons for allowance: With respect to claim 1, the claim has been found allowable over the prior art of record because the prior art of record fails to teach or fairly suggest a method for concurrently measuring multiple biological parameters in an animal, the method comprising: an absorption spectrum of the LSS fluorescent compound overlaps the absorption spectrum of the first GEFI, wherein an emission spectrum of the LSS fluorescent compound overlaps with an emission spectrum of the second GEFI; concurrently detecting fluorescence signals from the first GEFI, the second GEFI, and the LSS fluorescent compound using a multi-channel fluorescence sensing optical system; processing the detected fluorescence signals to determine values of the multiple biological parameters, wherein the processing reduces instrument and/or biological artifacts in the values of the multiple biological parameters in combination with the remaining limitations of the claim. With respect to claims 2-18, the claims have been found allowable due to its dependency to claim 1 above. Any comments considered necessary by applicant must be submitted no later than the payment of the issue fee and, to avoid processing delays, should preferably accompany the issue fee. Such submissions should be clearly labeled “Comments on Statement of Reasons for Allowance.” Comments: The closest prior art cited but not relied upon are listed herein: “Genetically Encoded Sensors for the In Vivo Detection of Neurochemical Dynamics” - Yang et al. discloses genetically encoded fluorescent Ca2+ indicator (see top paragraph of page 372 and first paragraph of section4 in page 373). The brightness of a fluorophore is determined primarily by two parameters, namely the extinction coefficient and quantum yield. The extinction coefficient describes the fluorophore’s efficiency at absorbing excitation light, while the quantum yield is the fluorophore’s ability to produce photons and is defined as the ratio of emitted photons to absorbed photons. Both parameters are intrinsic to the fluorophore’s chemical composition and can be affected by the microenvironment (see page 370, second paragraph in section 3). However, Yang is silent about having a long-Stokes-shift (LSS) fluorescent compound that is insensitive to the multiple biological parameters, wherein an absorption spectrum of the LSS fluorescent compound overlaps the absorption spectrum of the first GEFI, wherein an emission spectrum of the LSS fluorescent compound overlaps with an emission spectrum of the second GEFI. Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was filed to use a LSS fluorescent compound in combination with a genetically encoded fluorescent indicator as required by the current application in since the prior art system is not capable of imaging more than one biological parameter at once with low biological noise. There has not been a suitable method to account for various biological artifacts while imaging two spectrally orthogonal fluorescent proteins that capture two independent biological parameters as now required in the current application. This inability stifles the field from gaining new and accurate insight into the inner functioning of the brain. Accurate biological interpretation of data will be achieved if, and only if, unwanted biological artifacts are precisely monitored using a robust reference channel as done in the current invention. This approach allows unambiguous detection of signals from the three fluorophores with only two illumination sources. Using a NIR fluorophore would have required three illumination sources (and all additional opto-mechanical and electronic equipment). The current invention reduces the overall cost of the optical system by 50%. Thus, this technology provides a cost-effective method to multiplex fluorescence signals that uses a long Stokes shift fluorescent protein to reference the biological parameter under investigation. “Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals” – Haziza et al. discloses Fluorescence imaging studies of neural activity using genetically encoded voltage indicators (GEVIs) have generally focused on detecting neural action potentials (see page 4401, Introduction section). For dual-cell-type recordings, we used green and red GEVIs and a long Stokes-shift fluorescent protein, cyan-excitable orange-red fluorescent protein (cyOFP), that is excited by blue light, as is the green GEVI, but emits red fluorescence. Using two light sources modulated at distinct frequencies, uSMAART unambiguously separated signals from 3 fluors using 2 color channels (see page 4404, left column). However, Haziza uses genetically encoded voltage indicators as opposed to genetically encoded fluorescent indicators. Even though both use fluorescent proteins to visualize cellular activity, they differ fundamentally in what they measure and how they are designed. Therefore, the function differs from each other and it makes unobvious to use one in place of the other for perform the function claimed of obtaining absorption spectrum by excitation through the illumination. Instead, genetically encoded voltage indicators measure changes in a cell's transmembrane electrical potential. Furthermore, Haziza fails to discloses an absorption spectrum of the LSS fluorescent compound overlaps the absorption spectrum of the GEFI signals to determine values of the multiple biological parameters, wherein the processing reduces instrument and/or biological artifacts. In conclusion, Haziza fails to disclose, suggest the claim limitations by itself or in combination with Yang et al. above. “Novel genetically encoded biosensors for cGMP” Fabritius discusses encoded biosensors types and functions, including genetically encoded calcium indicators (GECIs) (page 32). Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to DIXOMARA VARGAS whose telephone number is (571)272-2252. The examiner can normally be reached Monday-Friday 8am-5pm. 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, Raymond Keith can be reached at 571-270-1790. 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. /DIXOMARA VARGAS/Primary Examiner, Art Unit 3798
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Prosecution Timeline

Nov 11, 2024
Application Filed
Jun 12, 2026
Non-Final Rejection mailed — §101 (current)

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Prosecution Projections

1-2
Expected OA Rounds
93%
Grant Probability
99%
With Interview (+8.4%)
2y 8m (~12m remaining)
Median Time to Grant
Low
PTA Risk
Based on 1011 resolved cases by this examiner. Grant probability derived from career allowance rate.

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