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 Status
Claims 1-20 are cancelled.
Claims 21-41 are newly added.
Claims 21-41 are currently pending and under exam herein.
Claims 21-41 are rejected.
Priority
The instant application is a continuation application of U.S. Application No. 17/826,762 filed 27 May 2022, which is a continuation application of U.S. Application No. 15/772,652 filed 1 May 2018, which is a National Stage Application under 35 U.S.C. 371 of co-pending PCT application PCT/US2016/060243 filed 3 November 2016, which claims the benefit of U.S. Provisional Application No. 62/250,255 filed 3 November 2015. Benefit is acknowledged. At this point in examination, the effective filing date of claims 21-41 is 3 November 2015.
Information Disclosure Statement
The information disclosure statements filed 23 January 2023 and 13 March 2025 fail to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. It has been placed in the application file, but the information referred to therein has not been considered.
The information disclosure statements (IDS) submitted on 8 April 2026, 11 November 2025, 27 August 2025, 12 June 2025, 13 March 2025, 12 December 2024, 26 September 2024, 27 November 2023, 12 September 2023, and 23 January 2023 comply with 37 CFR 1.98. Accordingly, all references listed have been considered by the examiner except where lined through.
Drawings
The drawings filed on 23 January 2023 have been received and are accepted.
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 21-41 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 21 recites the limitation "the sample" in ln. 4. There is insufficient antecedent basis for this limitation in the claim. Claim 21 recites the limitation "the plurality of target nucleic acids" in lns. 5-6. There is insufficient antecedent basis for this limitation in the claim. Claims 22-38 are similarly rejected due to their dependency on claim 21.
Claim 37 recites the limitation "the plurality of nucleic acids." There is insufficient antecedent basis for this limitation in the claim. Claim 37 will be interpreted to mean “the plurality of target nucleic acids.”
Claim 39 recites the limitation "the sample" in ln. 6. There is insufficient antecedent basis for this limitation in the claim. Claim 39 recites the limitation "the plurality of target nucleic acids" in lns. 7-8. There is insufficient antecedent basis for this limitation in the claim.
Claim 40 recites the limitation "the sample" in ln. 7. There is insufficient antecedent basis for this limitation in the claim. Claim 40 recites the limitation "the plurality of target nucleic acids" in lns. 8-9. There is insufficient antecedent basis for this limitation in the claim. Claim 41 is similarly rejected due to its dependency on claim 40.
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.
Claim 39 is rejected under 35 U.S.C. 101 because the claimed invention does not fall within one of the four enumerated categories of statutory subject matter. Claims 21-38 and 40-41 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (abstract ideas and natural phenomenon) without significantly more. Under MPEP § 2106, subject matter is patent eligible when the claimed invention is to one of the four statutory categories of invention [Step 1], and the claim is not directed to a judicial exception [Step 2A] unless the claim as a whole includes additional limitations amounting to significantly more than the exception [Step 2B].
Step 1
Claims 21-38 and 40-41 describe inventions that are to one of the statutory categories. In Step 1, a claim must fall within one of the four enumerated categories of statutory subject matter (process, machine, manufacture, or composition of matter); a claim falling outside these categories is ineligible without further analysis. See MPEP § 2106.03. Claims 21-38 are properly to one of the four statutory categories because the claimed invention is a method, which falls into the process category [Step 1: Yes]. Claims 40-41 are properly to one of the four statutory categories because the claimed invention is a system, which falls into the machine category [Step 1: Yes].
Claim 39 recites a “computer program product comprising a computer readable storage medium having program instructions embodied therewith.” While the specification states that the “computer-readable media may be and/or include one or more non-transitory computer-readable media,” at para. [0134], there is no limiting definition restricting the computer program product to only non-transitory computer-readable media. Absent a limiting definition, the broadest reasonable interpretation of a computer program product includes transitory forms of signal transmission. Transitory forms of signal transmission are not directed to any of the statutory categories. See MPEP § 2106.03(I). A claim whose broadest reasonable interpretation covers both statutory and non-statutory embodiments embraces subject matter that is not eligible for patent protection and therefore is directed to non-statutory subject matter. See MPEP § 2106.03(II). Therefore, claim 39 is not eligible for patent protection because it is directed to non-statutory subject matter when the broadest reasonable interpretation embraces transitory forms of signal transmission, which is not directed to any of the statutory categories.
Step 2A
Under Step 2A, a claim is directed to a judicial exception if, under the broadest reasonable interpretation, it recites an abstract idea, law of nature, or natural phenomena [Prong One] without the claim as a whole integrating the exception into a practical application [Prong Two]. Abstract ideas include mathematical concepts, mental processes, and certain methods of organizing human activity. Mathematical concepts encompass mathematical relationships, formulas, equations, and mathematical calculations. See MPEP § 2106.04(a)(2)(I). Mental processes involve concepts that can be performed in the human mind or by a human with the aid of pen and paper, such as observations, evaluations, judgments, or opinions. See MPEP § 2106.04(a)(2)(III). Certain methods of organizing human activity include fundamental economic principles, commercial or legal interactions, and managing personal behavior or relationships. See MPEP § 2106.04(a)(2)(II). Laws of nature and natural phenomena, include naturally occurring principles/relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature. See MPEP § 2106.04(b)-(c).
Prong One
A claim recites a judicial exception when it sets forth or describes a law of nature, natural phenomenon, or abstract idea. Claims 21-38 and 40-41 recite abstract ideas that fall into the groupings of mathematical concepts and mental processes.
Independent claims 21 and 40 recite the following limitations, which describe mathematical concepts and/or mental processes:
determining, using the plurality of light intensity values, relative positions of the plurality of target nucleic acids within the sample;
annotating a cellular or morphological feature of the first image of the stain of the sample with an annotation;
co-registering the first image of the stain of the sample with the relative positions of the plurality of target nucleic acids; and
generating, for display, a second image comprising the relative positions of the plurality of target nucleic acids and the annotation of the cellular or morphological feature.
Dependent claims 22-33 and 35-36 recite the following limitations, which narrow or describe abstract ideas and/or natural phenomenon:
Claim 22 recites wherein determining the relative positions of the plurality of target nucleic acids within the sample comprises determining point objects representing the plurality of light intensity values.
Claim 23 recites wherein determining the relative positions of the plurality of target nucleic acids within the sample comprises determining one or more image features.
Claim 24 recites wherein the one or more image features comprises a maximum radius, a mean radius, or a median radius.
Claim 25 recites wherein determining the relative positions of the plurality of target nucleic acids within the sample comprises determining one or more sequence features.
Claim 26 recites wherein the one or more sequence features comprises a quality score.
Claim 27 recites wherein the annotation is determined at a remote device.
Claim 28 recites wherein the annotation is determined at a local device.
Claim 29 recites wherein the annotation is determined from the stain of the sample.
Claim 30 recites wherein the annotation is a cellular feature of the first image of the stain of the sample.
Claim 31 recites wherein the annotation comprises at least one nuclei.
Claim 32 recites wherein the annotation comprises at least one cell membrane.
Claim 33 recites further comprising determining gene names at three-dimensional locations of the relative positions of the plurality of target nucleic acids.
Claim 35 recites generating, for display, the second image, the annotation of the cellular or morphological feature, and at least a portion of the three-dimensional locations of the relative positions of the plurality of target nucleic acids associated with the subset of the gene names.
Claim 36 recites wherein the plurality of light intensity values comprises a string of nucleic acid bases.
The independent claim limitation of determining relative positions involves processing or analyzing intensity data to compute or derive spatial positions. Such data analysis, signal processing, and position determination from raw measurements can be performed via generic algorithms, and can be performed mentally or with pen and paper at a high level of abstraction, which constitutes an abstract idea within the mathematical concepts and mental processes groupings. See MPEP §§ 2106.04(a)(I) & (a)(III). This abstract idea is narrowed by the limitations of dependent claims 22-26 because they specify how the relative positions are determined.
The independent claim limitation of annotating a cellular or morphological feature involves identifying, labeling, or classifying features in an image, which can be done by human observation, constituting an abstract idea within the mental processes grouping. See MPEP § 2106.04(a)(III). This abstract idea is narrowed by the limitations of dependent claims 27-32 because they specify the features to be annotated and where the annotation occurs. The independent claim limitation of co-registering the first image involves alignment, mapping, or spatial transformation between datasets/images, which constitutes an abstract idea within the mathematical concepts and mental processes groupings. See MPEP §§ 2106.04(a)(I) & (a)(III). The independent claim limitation of generating a second image involves generating a composite or overlaid image for display as a form of data presentation or visualization, which constitutes an abstract idea within the mental processes grouping. See MPEP § 2106.04(a)(III).
The limitation of dependent claim 33 involves sequence analysis from imaging data to identify/assign gene identities followed by spatial mapping, which can be performed mentally or with generic algorithms, constituting an abstract idea within the mathematical concepts and mental processes groupings. See MPEP §§ 2106.04(a)(I) & (a)(III). The limitation of dependent claim 35 involves data organization, selection, correlation, and presentation, which constitutes an abstract idea within the mathematical concepts and mental processes groupings. See MPEP §§ 2106.04(a)(I) & (a)(III). The limitation of dependent claim 36 reciting that the intensities comprise a base string involves the underlying relationship between florescence intensities and nucleotide identity, which is a natural phenomenon.
Dependent claims 34, 37-38, and 41 do not narrow or describe judicial exceptions, but inherit the judicial exceptions from the claims upon which they depend. Therefore, claims 21-38 and 40-41 recite judicial exceptions – namely abstract ideas within the mathematical concepts and mental processes groupings [Step 2A, Prong One: Yes].
Prong Two
Claims 21-38 and 40-41 as a whole do not integrate the recited judicial exception into a practical application. A claim that recites a judicial exception [Prong One] is deemed to be directed to a judicial exception [Step 2A] unless the claim as a whole contains additional elements that integrate the exception into a practical application [Prong Two]. A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. See MPEP §§ 2106.04(d) & 2106.05(e). A claim does not integrate a judicial exception into a practical application by reciting insignificant extra-solution activity, generally linking the exception to a particular technological environment or field of use, merely reciting to apply the exception, merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea. See MPEP § 2106.04(d)(I). Insignificant extra-solution activities are nominal or tangential additions to a claim that are incidental to the primary process or product, including both pre-solution and post-solution activity (e.g. pre-solution data gathering for use in a process). If integrated into a practical application, the claim is eligible; otherwise, it is directed to the judicial exception, necessitating further analysis at Step 2B.
Independent claims 21 and 40 recite the following limitations, which are additional elements:
a computing node comprising a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a processor to cause the processor to perform a method comprising
receiving volumetric imaging data from a plurality of sequencing cycles, wherein the volumetric imaging data comprises a plurality of light intensity values, wherein the plurality of light intensity values are associated with three-dimensional locations within the sample;
receiving a first image of a stain of the sample;
Dependent claims 34, 37-38, and 41 recite the following limitations, which are additional elements:
Claim 34 recites receiving a selection from a user of a subset of the gene names.
Claim 37 recites wherein the plurality of nucleic acids comprises a plurality of amplicons covalently bonded to a three-dimensional matrix.
Claim 38 recites wherein the stain is selected from the group consisting of: a nuclear stain, a membrane stain, and an antibody stain.
Claim 41 recites a display operably coupled to the computing node.
The independent claim limitations of receiving volumetric imaging data and receiving a first image constitute insignificant extra-solution activity that does not integrate the judicial exceptions into a practical application because they are mere data gathering step that do not transform the nature of the claim into a patent-eligible application of the judicial exception. See MPEP § 2106.05(g). Additionally, these limitations are data gathering steps that are limited to a particular type of data, which merely indicates a field of use or technological environment in which to apply a judicial exception and cannot integrate a judicial exception into a practical application. See MPEP § 2106.05(h). Similarly, the limitation of dependent claim 34 is an insignificant extra-solution data gathering step that indicates a field of use, and does not integrate the judicial exceptions into a practical application. The independent claim limitation of a computing node describes generic computer components that amount to nothing more than mere instructions to apply the judicial exceptions, which does not integrate into a practical application. See MPEP §§ 2106.05(b) & (f). Similarly, the limitation of dependent claim 41 describes generic computer components that amount to nothing more than mere instructions to apply the judicial exceptions, which does not integrate into a practical application.
The limitation of dependent claim 37 specifies the particular setting in which the abstract ideas are applied, which merely indicates a field of use or technological environment and cannot integrate a judicial exception into a practical application. See MPEP § 2106.05(h). The limitation of dependent claim 38 constitutes insignificant pre-solution activity because it specifies the type of stain, which is incidental to the primary process and merely a nominal or tangential addition to the claim. See MPEP § 2106.05(g). Finally, claims 22-33 and 35-36 do not include any additional elements.
The claims as a whole merely recite insignificant extra-solution activities, field of use limitations, and abstract ideas implemented on generic computer components without meaningful limitations that tie it to a specific technological improvement. Therefore, claims 21-38 and 40-41 do not contain additional elements that integrate the recited abstract ideas into a practical application [Step 2A, Prong Two: No].
Step 2B
Claims 21-38 and 40-41 do not include additional elements, whether considered individually or in combination, that are sufficient to amount to significantly more than the judicial exception itself. Under Step 2B, the claim is analyzed to determine whether there are any additional elements that, individually or in combination, constitute an “inventive concept" sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself. See MPEP § 2106.05; and Alice Corp. Pty. Ltd. v. CLS Bank Int'l, 573 U.S. 208, 217-18, 110 USPQ2d 1976, 1981 (2014).
Independent claims 21 and 40 recite the following limitations, which are additional elements:
a computing node comprising a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a processor to cause the processor to perform a method comprising
receiving volumetric imaging data from a plurality of sequencing cycles, wherein the volumetric imaging data comprises a plurality of light intensity values, wherein the plurality of light intensity values are associated with three-dimensional locations within the sample;
receiving a first image of a stain of the sample;
Dependent claims 34, 37-38, and 41 recite the following limitations, which are additional elements:
Claim 34 recites receiving a selection from a user of a subset of the gene names.
Claim 37 recites wherein the plurality of nucleic acids comprises a plurality of amplicons covalently bonded to a three-dimensional matrix.
Claim 38 recites wherein the stain is selected from the group consisting of: a nuclear stain, a membrane stain, and an antibody stain.
Claim 41 recites a display operably coupled to the computing node.
The independent claim limitations of receiving volumetric imaging data and receiving a first image constitute conventional insignificant extra-solution activity that merely indicates a field of use in which to apply the judicial exceptions and does not amount to significantly more than the exceptions themselves. See OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); and MPEP §§ 2106.05(d) & (g)-(h). Similarly, the limitation of dependent claim 34 is a conventional insignificant extra-solution data gathering step that indicates a field of use, and does not add significantly more than the exceptions themselves. See OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015); and MPEP §§ 2106.05(d) & (g)-(h). The independent claim limitation of a computing node describes conventional computer components that amount to nothing more than mere instructions to apply the judicial exceptions, which does not add significantly more than the exceptions themselves. See MPEP §§ 2106.05(b) & (f); and CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1368, 99 USPQ2d 1690, 1692 (Fed. Cir. 2011). Similarly, the limitation of dependent claim 41 describes conventional computer components that amount to nothing more than mere instructions to apply the judicial exceptions, which does not add significantly more than the exceptions themselves. See MPEP §§ 2106.05(b) & (f); and U.S. Patent No. 8405572B1, Abstract.
The limitation of dependent claim 37 specifies conventional setting in which the abstract ideas are applied, which merely indicates a field of use or technological environment and does not add significantly more. See MPEP § 2106.05(h); and Jun Zhu et al., Single Molecule Profiling of Alternative Pre-mRNA Splicing, 301 Science 836 col.2 para.1 (8 August 2003). The limitation of dependent claim 38 constitutes insignificant pre-solution activity because it specifies the type of stain, which are conventional and incidental to the primary process and merely a nominal or tangential addition to the claim. See MPEP § 2106.05(g); and Amelia Ruffatti et al., Nuclear membrane-staining antinuclear antibody in patients with primary biliary cirrhosis. 5(5) J Clin Immunol. 357, Abstract (13 May 1985).
Overall, claims 21-38 and 40-41 amount to no more than insignificant extra-solution activities and implementing the abstract ideas on conventional computers in a routine way. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception itself because the claims recite additional elements that equate to insignificant extra-solution activity and mere instructions to apply the recited abstract ideas in a generic way or in a generic computing environment. Therefore, claims 21-38 and 40-41 are rejected for failing to set forth patent eligible subject matter under 35 U.S.C. 101 because the claimed invention recites abstract ideas [Step 2A, Prong One: Yes] and the additional elements do not integrate the judicial exception into a practical application [Step 2A, Prong Two: No] and do not amount to claiming significantly more than the recited exception [Step 2B: No].
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.
Claims 21-23, 25-26, 29-31, 33, and 36-40 are rejected under 35 U.S.C. 103 as being unpatentable over Je Hyuk Lee et al., Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues, 10(3) Nat Protoc. (12 February 2015) (hereinafter “Lee”) in view of Rongqin Ke et al., In situ sequencing for RNA analysis in preserved tissue and cells, 10 Nat Methods 857-860 (14 July 2013) (hereinafter “Ke”), as evidenced by MathWorks, System Requirements - Release 2014a, (2015) (hereinafter “MathWorks”) and B I Tarnowski et al., DAPI as a useful stain for nuclear quantitation, 66(6) Biotech Histochem. (1991) (hereinafter “Tarnowski”).
Regarding independent claims 21 and 39-40, Lee discloses a method of fluorescent in situ sequencing (FISSEQ) for the detection of tissue specific gene expression, RNA splicing, and post-transcriptional modifications while preserving spatial context. At 442 col.1 para.2. Lee teaches receiving multi-cycle sequencing-by-ligation imaging data, which capture fluorescence intensity values located at 3D positions within the sample. At 446 col.2 para.2 – 448 col.1 para.2 (receiving volumetric imaging data from a plurality of sequencing cycles, wherein the volumetric imaging data comprises a plurality of light intensity values, wherein the plurality of light intensity values are associated with three-dimensional locations within the sample). Lee discloses processing fluorescence intensity signals across sequencing cycles to determine centroid positions of amplicons in the sample. At 442 col.2 para.3; 448 col.1 paras.3-4 (determining, using the plurality of light intensity values, relative positions of the plurality of target nucleic acids within the sample). Lee discloses obtaining a DAPI staining of the sample. At 457 para.4; Figure 6 (receiving a first image of a stain of the sample). Lee teaches that the pipeline identifies and distinguishes cellular/morphological features, and annotates cellular compartments in the image with labels for cytoplasm vs. nucleus. At 445 col.1 para.3 & col.2 para.1; Figure 3; 457 para.4 (annotating a cellular or morphological feature of the first image of the stain of the sample with an annotation). Lee discloses that the software registers the images, including the stain image, and aligns pixels to the reference sequence for relative position. At 448 col.1 para.3; Figures 4-6 (co-registering the first image of the stain of the sample with the relative positions of the plurality of target nucleic acids). Lee teaches that the pipeline generates a registered image and a file containing gene ID, name, cluster size, strand, class, base quality, alignment quality, color space sequence and x-y position. At 457 para.4; Figure 3a (generating, for display, a second image). Lee fails to teach the second image comprising the relative positions of the plurality of target nucleic acids and the annotation of the cellular or morphological feature.
However, Ke discloses an image analysis pipeline for base-calling, in which images from consecutive sequencing cycles are automatically aligned and fluorescence intensities are measured at every position corresponding to a sequencing substrate. At 857 col.2 para.2. Ke teaches generating an image comprising the spatial location of target nucleotides, gene name, and an indication of cellular/morphological features. At 859 col.1 para.1; Figure 3. Lee discloses a pipeline for multi-cycle sequencing, deriving relative positions from light intensity values, image restoration across cycles, morphological context via DAPI, and generation of composite visualizations. Ke teaches a technique for data presentation where relevant information is directly overlaid on a histological stain image. A person having ordinary skill in the art would recognize that Ke’s data visualization technique can be applied to Lee’s pipeline to predictably yield an improved pipeline that generates a more integrated composite image in which relative positions and morphological annotations are visually combines on the stain image itself. Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007); and MPEP § 2143, D.
Claim 39 additionally recites a computer program product comprising a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a processor. Claim 40 additionally recites a system comprising: a computing node comprising a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a processor. Lee discloses a complete software-based analysis pipeline using METLAB scripts, R, Bowtie for alignment, custom image processing code, and Imaris for visualization. At 442 col.2 para.3; 448 col.1 paras.1 & 4. These are program instructions stored on and executed from computer-readable media (hard drives, servers, etc.) by processors to carry out the entire workflow. Thus, the disclosure of Lee inherently includes a computer readable storage medium having program instructions to be executed by a processor, as evidenced by MathWorks. See Windows table.
Regarding claim 22, Lee discloses processing fluorescence intensity signals across sequencing cycles to determine centroid positions of amplicons in the sample. At 442 col.2 para.3; 448 col.1 paras.3-4 (the method of claim 21, wherein determining the relative positions of the plurality of target nucleic acids within the sample comprises determining point objects representing the plurality of light intensity values).
Regarding claim 23, Lee discloses that the pipeline determines relative positions by first performing image processing on the light intensity data. At 448 col.1 paras.2-3. As part of that process, the number of individual pixels per object is determined, which directly relates to cluster size. At 442 col.2 para.3; 448 col.1 para.4; Figure 5 (the method of claim 21, wherein determining the relative positions of the plurality of target nucleic acids within the sample comprises determining one or more image features).
Regarding claim 25, Lee discloses that the pipeline determines relative positions by first performing image processing on the light intensity data. At 448 col.1 paras.2-3. After base calling, sequence features such as base call quality and alignment quality are determined as part of the process that produces the relative positions of the amplicon objects. At 442 col.2 para.3 (the method of claim 21, wherein determining the relative positions of the plurality of target nucleic acids within the sample comprises determining one or more sequence features).
Regarding claim 26, Lee discloses that sequence features such as base call quality and alignment quality are determined as part of the process that produces the relative positions of the amplicon objects. At 442 col.2 para.3 (the method of claim 25, wherein the one or more sequence features comprises a quality score).
Regarding claim 29, Lee discloses using DAPI stains to generate masks that define cellular/morphological compartments, which are used to annotate the spatial context of the sequenced reads. At 457 para.4; Figure 3 (the method of claim 21, wherein the annotation is determined from the stain of the sample).
Regarding claims 30-31, Lee discloses annotating the nucleus and cytoplasm of the DAPI stain image. Figure 3 (the method of claim 21, wherein the annotation is a cellular feature of the first image of the stain of the sample; the method of claim 21, wherein the annotation comprises at least one nuclei).
Regarding claim 33, Lee discloses assigning gene names to the relative positions. At 448 col.1 para.4; 457 para.4 (the method of claim 21, further comprising determining gene names at three-dimensional locations of the relative positions of the plurality of target nucleic acids).
Regarding claim 36, Lee teaches that the light intensities from imaging are cDNA amplicons. At 442 col.2 para.1; Figure 1 (the method of claim 21, wherein the plurality of light intensity values comprises a string of nucleic acid bases).
Regarding claim 37, Lee discloses that the target nucleobases are amplicons that are cross-linked to create a highly porous and 3D nucleic acid matrix inside the cell. At 442 col.2 para.1 (the method of claim 21, wherein the plurality of nucleic acids comprises a plurality of amplicons covalently bonded to a three-dimensional matrix).
Regarding claim 38, Lee discloses using a 4',6-diamidino-2-phenylindole (DAPI) stain. At 457 para.4; Figure 6. DAPI is a nuclear stain, as evidenced by Tarnowski. Abstract (the method of claim 21, wherein the stain is selected from the group consisting of: a nuclear stain, a membrane stain, and an antibody stain).
Claim 24 is rejected under 35 U.S.C. 103 as being unpatentable over Lee and Ke as applied to claims 21-23, 25-26, 29-31, 33, and 36-40 above, and further in view of Mark-Anthony Bray et al., Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images, Curr. Protoc. Mol. Biol. 109:14.17.1-14.17.13. (January 2015) (hereinafter “Bray”) and Lee Kamentsky, cellprofiler/modules/measureobjectsizeshape.py, GitHub (6 February 2015) (hereinafter “Kamentsky”).
Regarding claim 24, Lee fails to disclose determining relative positions by determining a maximum radius, a mean radius, or a median radius. However, Bray discusses image analysis using the software CellProfiler. At 1 para.2. Bray discloses that MeasureObjectSizeShape can be used to determine features of images. At 9 para.4. MeasureObjectSizeShape can measure maximum radius, median radius, and mean radius, as evidenced by Kamentsky. At ln.62-67. Lee discloses a pipeline for multi-cycle sequencing, deriving relative positions from light intensity values, image restoration across cycles, morphological context via DAPI, and generation of composite visualizations. CellProfiler is an open-source image analysis tool for feature extraction. A person having ordinary skill in the art would recognize that CellProfiler can be integrated into the pipeline of Lee to compute additional standard morphological descriptors that would result in an improved pipeline when the additional features support improved object tracking. Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007); and MPEP § 2143, D.
Claims 27-28 and 40 are rejected under 35 U.S.C. 103 as being unpatentable over Lee and Ke as applied to claims 21-23, 25-26, 29-31, 33, and 36-40 above, and further in view of Chris Allan et al., OME Remote Objects (OMERO): a flexible, model-driven data management system for experimental biology, 9(3) Nat Method. 245–53 (10 September 2012) (hereinafter “Allan”).
Regarding claims 27-28, Lee fails to specify whether the annotation is determines at a remote or local device. However, Allan discloses Open Microscopy Environment Remote Objects (OMERO), which is a software platform designed for biological image data that supports visualization, annotation, analysis, and data sharing. At 5 para.1. OMERO supports image annotation at local devices and remote devices. Figures 1-2. Lee discloses a pipeline for multi-cycle sequencing, deriving relative positions from light intensity values, image restoration across cycles, morphological context via DAPI, and generation of composite visualizations. Allan discloses a client-server platform designed for biological image data that supports visualization, annotation, analysis, and data sharing. A person having ordinary skill in the art would have recognized that Lee’s pipeline can be implemented on OMERO to result in an improved client-server system that is flexible and allows users to perform annotations remotely or locally. Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007); and MPEP § 2143, D.
Regarding claim 41, Allan discloses that the computing system is operably coupled to a display. At 3 para.3 (the system of claim 40, further comprising a display operably coupled to the computing node).
Claim 32 is rejected under 35 U.S.C. 103 as being unpatentable over Lee and Ke as applied to claims 21-23, 25-26, 29-31, 33, and 36-40 above, and further in view of Je Hyuk Lee et al., Highly Multiplexed Subcellular RNA Sequencing in Situ, 343(6177) Science (21 March 2014) (hereinafter “original report”).
Regarding claim 32, Lee does not explicitly disclose the annotation comprises at least one cell membrane. However, Lee notes that the disclosed protocol details the methods described in their original report. At 445 col.2 para.2. The original report discloses that the amplicons can be stained to determine subcellular structures, such as the plasma membrane, the nuclear membrane, the nucleolus, and the chromatin. At 1360 col.3 para.1. A person having ordinary skill in the art would be motivated to annotate the nuclear membrane as suggested by the original report. One of ordinary skill in the art would reasonably expect success because the pipeline of Lee details the methods described in the original report. Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007); and MPEP § 2143, G.
Claims 34-35 are rejected under 35 U.S.C. 103 as being unpatentable over Lee and Ke as applied to claims 21-23, 25-26, 29-31, 33, and 36-40 above, and further in view of Andrew Zaldivar and Jeffrey L. Krichmar, Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool, 8(51) Front. Neuroinform. (20 May 2014) (hereinafter “Zaldivar”).
Regarding claim 34, Lee fails to teach receiving a selection from a user of a subset of the gene names. However, Zaldivar discloses a web-based interactive visualization platform for spatial gene expression data. Abstract. Zaldivar teaches that users can select a list of genes to explore, and the system will display the information relevant to the selected genes. At 3 col.1 paras.2-3. Zaldivar notes that this system allows users to immediately obtain data relevant to the genes of interest. At 2 col.1 para.2. A person having ordinary skill in the art would be motivated to modify the pipeline of Lee to include a user-selection feature, as taught by Zaldivar, to predictably yield an improved pipeline where users are able to focus on the genes of interest. Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007); and MPEP § 2143, G.
Regarding claim 35, Ke teaches generating an image comprising the spatial location of target nucleotides, gene name, and an indication of cellular/morphological features. At 859 col.1 para.1; Figure 3. When combined with the teachings of Zaldivar regarding user-selected genes, one of ordinary skill in the art would understand that the relative positions displayed should be focused on those associated with the user-selected genes.
Conclusion
No claim is allowed.
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/E.A.D./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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