DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Preliminary Amendment
The amendment submitted 3/5/2025 has been accepted and entered. Claims 1-21 are cancelled. No claims are amended. New claims 22-44 are added. Thus, claims 22-44 are examined.
Specification
The term “substantially the same resolution” is defined in the Specification establishes how to measure the resolution of axially-displaced planes in paragraphs [0007], [0163]).
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.
Claim(s) 22-26, 31-32, 38-44 is/are rejected under 35 U.S.C. 103 as being unpatentable over Buermann et al (US 20130260372 A1).
Regarding claim 22, Buermann et al discloses a system (100) configured to image at least two sample planes (172)(174) (paragraph [0050]), the system comprising: an objective lens (101); a flow cell (170); and at least one image sensor (108) configured to obtain images of the at least two sample planes within said flow cell, wherein the at least two sample planes are axially-displaced from one another along an optical axis of the objective lens (z-direction) (See Figs. 2-3), wherein the imaging system has a numerical aperture (NA) of less than 0.6 (0.2, 0.3, 0.4, 0.5) (paragraph [0047]) and a field-of-view (FOV) of greater than 1.0 square millimeters (mm²) (paragraphs [0030], [0046]), wherein the images of the at least two sample planes have substantially the same resolution (paragraph [0041]). In a first embodiment Buermann et al teaches systems configured to image the sample planes in the alternative not a single system configured to image both sample planes, wherein the images of the at least two sample planes have substantially the same resolution. However, Buermann discloses a second embodiment wherein both sample planes are imaged (paragraph [0059]). Buermann further teaches the objective can be moved in the z direction to alter focus (paragraph [0051]) (i.e. as the imaging of two planes would use the same image optics, sliding the objective so that each sample plane is in focus would generate images having the same or substantially the same direction). Thus, it would have been obvious to one of ordinary skill in the art to have modified the first embodiment of Buermann et al in view of the further teachings of Buermann et al to image both sample planes such that the images of the at least two sample planes have substantially the same resolutions so as to increase the amount of imaging data collected as compared to only imaging one sample plane.
Regarding claim 23, Buermann et al discloses wherein the system comprises two imaging channels wherein each imaging channel of the two or more imaging channels comprises an NA of greater than 0.2 (0.2, 0.3, 0.4, 0.5) (paragraph [0047]).
Regarding claim 24, Buermann et al discloses wherein the system comprises two imaging channels, wherein each imaging channel of the two imaging channels comprises a FOV of greater than 1 mm² (1 mm² or more of an array) (paragraphs [0030], [0046]).
Regarding claim 25, Buermann et al discloses wherein an imaging channel of the two or more imaging channels has an optical resolution of at least 1 micrometer over the FOV of the imaging channel (paragraphs [0030], [0046], [0051]).
Regarding claim 26, Buermann et al discloses wherein the system comprises two imaging channels, wherein each imaging channel of the two channels comprises a FOV of at least 1 mm in a spatial dimension (paragraphs [0030], [0046], [0051]).
Regarding claim 31, Buermann et al discloses wherein said at least two sample planes comprise at least two surfaces (paragraph [0030]).
Regarding claim 32, Buermann et al discloses wherein the at least two sample planes comprise two or more sample planes separated along a z direction (See Figs. 2-3 and paragraph [0130]).
Regarding claim 38, Buermann et al discloses wherein further comprising one or more samples affixed to a surface of at least two surfaces (paragraph [0149]).
Regarding claim 39, Buermann et al discloses wherein the one or more samples are derived from a cell or a tissue (paragraph [0149]).
Regarding claim 40, Buermann et al discloses wherein the one or more samples comprise one or more nucleic acid molecules (paragraph [0067]).
Regarding claim 41, Buermann et al discloses wherein the system is configured to image the one or more samples for sequencing analysis (paragraphs [0093]).
Regarding claim 42, Buermann et al discloses wherein the at least one image sensor (plurality of microfluorometers) is configured to image fluorescent signals emitted from the one or more samples (paragraph [0092]).
Regarding claim 43, Buermann et al discloses wherein the one or more samples comprise one or more cells or tissues (paragraph [0149]).
Regarding claim 44, Buermann et al discloses wherein the system comprises two or more imaging channels configured to each image different wavelengths (paragraph [0092]).
Claim(s) 27-30, 33-37 is/are rejected under 35 U.S.C. 103 as being unpatentable over Buermann et al (US 20130260372 A1) in view of Ghorbani et al (CN 117980503 A).
Regarding claim 27, Buermann et al discloses all of the limitations of parent claim 22, as described above however, Buermann et al is silent with regards to diffraction-limited over at least 60% of FOV as claimed. Ghorbani et al discloses an optical system for nucleic acid sequencing and method, comprising: imaging channel of two or more imaging channels comprise a field of view that is diffraction-limited over at least 60% of FOV (objective lens (110) configured to provide a FOV to the fluorescence imaging module such that the FOV has diffraction limited performance such as, i.e. between 60% to 100%) (page 43). Thus, it would have been obvious to modify Buermann et al with the teaching of Ghorbani et al so as to enable high-speed, large-area imaging with high quality resolution.
Regarding claim 28, Buermann et al in view of Ghorbani et al discloses wherein the system comprises two or more imaging channels, wherein each imaging channel of the plurality of imaging channels comprises a field of view that has less than 0.15 waves of aberration over at least 60% of the FOV (page 43). Thus, it would have been obvious to modify Buermann et al with the teaching of Ghorbani et al so as to eliminate constant physical refocusing.
Regarding claim 29, Buermann et al in view of Ghorbani et al discloses the system is configured to acquire one or more flow cell images of said flow cell in a FOV of greater than 1 mm² at a sample plane in each of the two or more imaging channels in less than 30 seconds (pages 87-88).
Regarding claim 30, Buermann et al in view of Ghorbani et al discloses wherein the system comprises two or more imaging channels, wherein the system is configured to have a sequencing cycle time of acquiring one or more flow cell images of said flow cell in a FOV of greater than 1 mm² at a sample plane in each of the two or more imaging channels is less than 3 minutes (page 93). Thus, it would have been obvious to modify Buermann et al with the teaching of Ghorbani et al, so as to accelerate high-throughput genetic sequencing.
Regarding claim 33, Buermann et al in view of Ghorbani et al discloses wherein the system is configured to image one or more samples for nucleic acid sequencing, wherein the one or more samples comprise nucleic acid molecules or clusters thereof with a surface density of greater than 1x 10⁵ molecules or clusters per mm² (page 89).
Regarding claim 34, Buermann et al in view of Ghorbani et al discloses wherein image one or more samples comprising hybridized oligonucleotide molecules with a surface density of at least 1x 10⁵ molecules per mm² for nucleic acid sequencing (page 86). Thus, it would have been obvious to modify Buermann et al with the teaching of Ghorbani et al, so as to improve signal to noise ratio.
Regarding claim 35, Buermann et al in view of Ghorbani et al discloses wherein the system is configured to sequence one or more samples comprising oligonucleotide molecules with a surface density of at least 0.01 molecules per square micrometer (um²) (page 84). Thus, it would have been obvious to modify Buermann et al with the teaching of Ghorbani et al, so as to prevent optical overlap.
Regarding claim 36, Buermann et al in view of Ghorbani et al discloses wherein the system is configured to image one or more samples on a support surface for nucleic acid sequencing, wherein a surface density of oligonucleotide adapter or primer is at most 1 X 10⁶ adapter or primer molecules per um². Thus, it would have been obvious to modify Buermann et al with the teaching of Ghorbani et al, so as to prevent optical and spatial crowding during imaging.
Regarding claim 37, Buermann et al in view of Ghorbani et al discloses wherein an optical system for nucleic acid sequencing and method, comprising: image one or more sample for nucleic acid sequencing, wherein the one or more samples are administered with a concentration of nucleic acid molecules in a range from 90 picomolar (pM) to 200 nanomolar (nM) (i.e. 10pM to 200 nm) (Fig. 58). Thus, it would have been obvious to modify Buermann et al with the teaching of Ghorbani et al, so as to prevents overlapping fluorescent signals on a dense flow cell while ensuring there are enough target molecules to saturate the imaging field of view (FOV).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Williamson et al (US 11697116 B2) discloses a device for biological analysis comprising: widefield imaging, specific numerical apertures, and flow cells with axially displaced imaging planes to map or sequence samples.
Daugharthy et al (US 11542554 B2) discloses volumetric imaging system comprising: objective lenses and image sensors configured to obtain images of multiple axially displaced planes within a flow cell.
Buermann et al (US 2020/0139375 A1) discloses an integrated microfluorometer design is that the microfluorometer can be conveniently moved, for example in a scanning operation, to allow imaging of a substrate that is larger than the field of view of the microfluorometer. Several microfluorometers can be combined to form a read head (1000) (See Fig. 8). A sequencing method or apparatus can use single color detection. For example, microfluorometer or read head need only provide excitation at a single wavelength or in a single range of wavelengths. Thus, a microfluorometer or read head need only have a single excitation source and multiband filtration of excitation need not be necessary. For a nucleotide delivery configuration where delivery results in multiple different nucleotide being present in the flow cell at one time, features that incorporate different nucleotide types can be distinguished based on different fluorescent labels that are attached to respective nucleotide types in the mixture. For example, four different nucleotide can be used, each having one of four different fluorophores. In one embodiment the four different fluorophores can be distinguished using excitation in four different regions of the spectrum. For example, a microfluorometer or read head can include four different excitation radiation sources.
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/F.P.B./Examiner, Art Unit 2884
/UZMA ALAM/Supervisory Patent Examiner, Art Unit 2884
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