Patent Application 17759357 - METHODS AND COMPOSITIONS FOR RETRIEVING CELLULAR - Rejection

Patent Application 17759357 - METHODS AND COMPOSITIONS FOR RETRIEVING CELLULAR

Title: METHODS AND COMPOSITIONS FOR RETRIEVING CELLULAR STRUCTURES BASED ON SPATIOTEMPORAL PROFILES

Application Information

• Invention Title: METHODS AND COMPOSITIONS FOR RETRIEVING CELLULAR STRUCTURES BASED ON SPATIOTEMPORAL PROFILES
• Application Number: 17759357
• Submission Date: 2025-04-08T00:00:00.000Z
• Effective Filing Date: 2022-07-22T00:00:00.000Z
• Filing Date: 2022-07-22T00:00:00.000Z
• National Class: 382
• National Sub-Class: 133000
• Examiner Employee Number: 88403
• Art Unit: 2877
• Tech Center: 2800

Rejection Summary

• 102 Rejections: 1
• 103 Rejections: 7

Cited Patents

The following patents were cited in the rejection:

• US 0120931🔗
• US 0286181🔗
• US 0028605🔗
• US 0060121🔗
• US 0030434🔗

Office Action Text

    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 .
Election/Restrictions
Applicant’s election of Group I in the reply filed on March 3, 2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
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) is/are: 
“imaging the plurality of structures using the imaging system” in claim 1 and
“structure sorting system” in claim 2.
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 § 102
In the event the determination of the status of the application as subject to AIA  35 U.S.C. 102 and 103 (or as subject to pre-AIA  35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA  to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.  
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –

(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.


(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.

Claims 1-4 are rejected under 35 U.S.C. 102(a)(1),(a)(2) as being anticipated by Lombana et al (US 2018/0030434 A1), hereinafter “Lombana”.
Regarding claim 1, Lombana discloses a method for screening cellular, subcellular, or multicellular structures (abstract; Figs. 17A, 17B; paragraphs [0059],[0085]), comprising the steps of:
a) introducing a plurality of cellular, subcellular, or multicellular structures, or a combination thereof, to an imaging system (Fig. 17B, paragraph [0085]), wherein one or more structures of the plurality comprise one or more taggable markers (paragraph [0208]);
b) imaging the plurality of structures using the imaging system (paragraph [0085], Fig. 17B);
c) identifying one or more target structures among the plurality of structures based on one or more properties of the target structures (paragraphs [0028], [0085]);
d) tagging the target structures to produce tagged target structures (paragraph [0085]), wherein each target structure is selectively illuminated by an excitation light (paragraph [0085]), thereby causing one or more taggable markers within the target structure to be phototransformed to produce one or more phototransformed taggable markers within the target structure (paragraph [0085]); and
e) isolating one or more tagged target structures from the plurality of structures using the phototransformed taggable markers (Fig. 17B).
Regarding claim 2, Lombana discloses wherein the isolation of the one or more tagged target structures is performed with a structure sorting system (paragraph [0085], Fig. 17B).
Regarding claim 3, Lombana discloses wherein the structure sorting system is a flow cytometer with sorting capability (paragraph [0085], Fig. 17B).
Regarding claim 4, Lombana discloses wherein the structure sorting system is a fluorescence-activated large particle sorter (paragraph [0397], [0005]).
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.

The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary.  Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Lombana as applied to claim 1 above.
Regarding claim 8, Lombana is silent regarding wherein steps a)-d) are repeated one or more times prior to isolation in step e).
However, it would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to include wherein steps a)-d) are repeated one or more times prior to isolation in step e) as it has been held that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSR International Co. v. Teleflex Inc. (KSR) at 550 U.S. 398, 415-16, 82 USPQ2d 1385, 1395 (2007). One would be motived to repeat the steps in order to have increased accuracy before performing the sorting.
Claims 9-11 are rejected under 35 U.S.C. 103 as being unpatentable over Lombana as applied to claim 1 above, and further in view of Betzig et al. (US 2013/0286181 A1), hereinafter
 “Betzig”.
Regarding claim 9, Lombana is silent regarding wherein the one or more taggable markers comprise a phototransformable protein.
However, Betzig teaches microscope illumination (abstract) including wherein the one or more taggable markers comprise a phototransformable protein (paragraphs [0165]-[0167]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Betzig by including wherein the one or more taggable markers comprise a phototransformable protein in order to detect the desired sample. 
Regarding claim 10, Lombana is silent regarding wherein the phototransformable protein is a photoactivatable protein.
However, Betzig teaches microscope illumination (abstract) including wherein the phototransformable protein is a photoactivatable protein (paragraphs [0165]-[0167]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Betzig by including wherein the phototransformable protein is a photoactivatable protein in order to detect the desired sample. 
Regarding claim 11, Lombana is silent regarding wherein the photoactivatable protein is selected from the group consisting of: PA-GFP, PA-sfGFP, PAmCherry1, PATagRFP, PAmKate, and Phamret.
However, Betzig teaches microscope illumination (abstract) including wherein the photoactivatable protein is selected from the group consisting of: PA-GFP, PA-sfGFP, PAmCherry1, PATagRFP, PAmKate, and Phamret (paragraphs [0165]-[0167]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Betzig by including wherein the photoactivatable protein is selected from the group consisting of: PA-GFP, PA-sfGFP, PAmCherry1, PATagRFP, PAmKate, and Phamret in order to detect the desired sample.
Claims 12-13, 23-34 are rejected under 35 U.S.C. 103 as being unpatentable over Lombana as applied to claim 1 above, and further in view of Hasle, Nicholas, et al. "Visual cell sorting: a high-throughput, microscope-based method to dissect cellular heterogeneity." BioRxiv (2019): 856476, hereinafter “Hasle”.
Regarding claim 12, Lombana is silent regarding wherein the phototransformable protein is a photoconvertable protein.
However, Hasle teaches particle detection (abstract) wherein the phototransformable protein is a photoconvertable protein (page 4-5, Results).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the phototransformable protein is a photoconvertable protein in order to detect the desired sample..
Regarding claim 13, Lombana is silent regarding wherein the photoconvertable protein is selected from the group consisting of: Kaede, Dendra2, mClavGR2, mMaple, PS-CFP2, Meos3.2, EosFP, mEosFP, mEos2, mEos3.2, mEos4a, mEos4b, tdEos, kikGR, PsmOrange, PsmOrange2, and mKikGR.
However, Hasle teaches particle detection (abstract) wherein the photoconvertable protein is selected from the group consisting of: Kaede, Dendra2, mClavGR2, mMaple, PS-CFP2, Meos3.2, EosFP, mEosFP, mEos2, mEos3.2, mEos4a, mEos4b, tdEos, kikGR, PsmOrange, PsmOrange2, and mKikGR (page 4-5, Results).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the photoconvertable protein is selected from the group consisting of: Kaede, Dendra2, mClavGR2, mMaple, PS-CFP2, Meos3.2, EosFP, mEosFP, mEos2, mEos3.2, mEos4a, mEos4b, tdEos, kikGR, PsmOrange, PsmOrange2, and mKikGR in order to detect the desired sample.
Regarding claim 23, Lombana is silent regarding wherein the plurality of structures are prokaryotic or eukaryotic cells.
However, Hasle teaches particle detection (abstract) wherein the plurality of structures are prokaryotic or eukaryotic cells (page 16, Cell Lines).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the plurality of structures are prokaryotic or eukaryotic cells in order to detect the desired sample.
Regarding claim 24, Lombana is silent regarding wherein the plurality of structures are from an animal, from a plant, from a fungus, from a protist, from a bacteria, from a yeast, or from a mixture thereof.
However, Hasle teaches particle detection (abstract) wherein the plurality of structures are from an animal, from a plant, from a fungus, from a protist, from a bacteria, from a yeast, or from a mixture thereof (page 16, Cell Lines).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the plurality of structures are from an animal, from a plant, from a fungus, from a protist, from a bacteria, from a yeast, or from a mixture thereof in order to detect the desired sample.
Regarding claim 25, Lombana is silent regarding wherein the plurality of structures are from a mammal.
However, Hasle teaches particle detection (abstract) wherein the plurality of structures are from a mammal (page 16, Cell Lines).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the plurality of structures are from a mammal in order to detect the desired sample.
Regarding claim 26, Lombana is silent regarding wherein the structures are from a human.
However, Hasle teaches particle detection (abstract) wherein the structures are from a human (page 3, Introduction).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the structures are from a human in order to detect the desired sample..
Regarding claim 27, Lombana is silent regarding wherein the human is known to have a medical condition or is suspected of having a medical condition.
However, Hasle teaches particle detection (abstract) wherein the human is known to have a medical condition or is suspected of having a medical condition (page 11).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the human is known to have a medical condition or is suspected of having a medical condition in order to detect the desired sample.
Regarding claim 28, Lombana is silent regarding wherein one or more structures in the plurality comprise a vector.
However, Hasle teaches particle detection (abstract) wherein one or more structures in the plurality comprise a vector (pages 42-43).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein one or more structures in the plurality comprise a vector in order to detect the desired sample.
Regarding claim 29, Lombana is silent regarding wherein the vector comprises an expression construct that encodes a mutant of a wild type protein.
However, Hasle teaches particle detection (abstract) wherein the vector comprises an expression construct that encodes a mutant of a wild type protein (pages 42-43).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the vector comprises an expression construct that encodes a mutant of a wild type protein in order to detect the desired sample.
Regarding claim 30, Lombana is silent regarding wherein the one or more properties of the target structures are selected from the group consisting of fluorescence, bioluminescence, morphology, size, granularity, localization, calcium concentration, voltage, and a combination thereof.
However, Hasle teaches particle detection (abstract) wherein the one or more properties of the target structures are selected from the group consisting of fluorescence, bioluminescence, morphology, size, granularity, localization, calcium concentration, voltage, and a combination thereof (pages 10-11).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the one or more properties of the target structures are selected from the group consisting of fluorescence, bioluminescence, morphology, size, granularity, localization, calcium concentration, voltage, and a combination thereof in order to detect the desired sample.
Regarding claim 31, Lombana is silent regarding further comprising the step of: e) analyzing the one or more isolated tagged target structures.
However, Hasle teaches particle detection (abstract) further comprising the step of: e) analyzing the one or more isolated tagged target structures (pages 9-10).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including further comprising the step of: e) analyzing the one or more isolated tagged target structures in order to detect the desired sample.
Regarding claim 32, Lombana is silent regarding wherein the analyzing comprises analysis of one or more DNA or RNA sequences in the one or more isolated tagged target structures.
However, Hasle teaches particle detection (abstract) wherein the analyzing comprises analysis of one or more DNA or RNA sequences in the one or more isolated tagged target structures (pages 9-10).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein the analyzing comprises analysis of one or more DNA or RNA sequences in the one or more isolated tagged target structures in order to detect the desired sample.
Regarding claim 33, Lombana is silent regarding wherein one or more structures comprise a vector that comprises an expression construct that encodes a mutant of a wild type protein, and wherein at least part of the sequence of the mutant is determined.
However, Hasle teaches particle detection (abstract) wherein one or more structures comprise a vector that comprises an expression construct that encodes a mutant of a wild type protein, and wherein at least part of the sequence of the mutant is determined (pages 9-10).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including wherein one or more structures comprise a vector that comprises an expression construct that encodes a mutant of a wild type protein, and wherein at least part of the sequence of the mutant is determined in order to detect the desired sample.
Regarding claim 34, Lombana is silent regarding further comprising the step of culturing the one or more isolated tagged target structures.
However, Hasle teaches particle detection (abstract) further comprising the step of culturing the one or more isolated tagged target structures (page 38).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Hasle by including further comprising the step of culturing the one or more isolated tagged target structures in order to detect the desired sample.
Claims 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Lombana as applied to claim 1 above, and further in view of Chouket et al. (US 2023/0028605 A1), hereinafter “Chouket”.
Regarding claim 14, Lombana is silent regarding wherein the phototransformable protein is a photoswitchable protein.
However, Chouket teaches particle detection (abstract) wherein the phototransformable protein is a photoswitchable protein (paragraphs [0006], [0152]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Chouket by including wherein the phototransformable protein is a photoswitchable protein in order to detect the desired sample.
Regarding claim 15, Lombana is silent regarding wherein the photoswitchable protein is selected from the group consisting of: mTFP0.7, PDM1-4, Dronpa, Dronpa-2, Dronpa-3, bsDronpa, Padron, Padron0.9, Mut2Q, rsFastLime, rsKame, Dreiklang, mGeos-M, EYQ1, KFP1, rsCherry, rsCherryRev, rsTagRFP, mApple, asFP595, Kindling FP, rseGFP, and rseGFP2.
However, Chouket teaches particle detection (abstract) wherein the photoswitchable protein is selected from the group consisting of: mTFP0.7, PDM1-4, Dronpa, Dronpa-2, Dronpa-3, bsDronpa, Padron, Padron0.9, Mut2Q, rsFastLime, rsKame, Dreiklang, mGeos-M, EYQ1, KFP1, rsCherry, rsCherryRev, rsTagRFP, mApple, asFP595, Kindling FP, rseGFP, and rseGFP2 (paragraphs [0006], [0152]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Chouket by including wherein the photoswitchable protein is selected from the group consisting of: mTFP0.7, PDM1-4, Dronpa, Dronpa-2, Dronpa-3, bsDronpa, Padron, Padron0.9, Mut2Q, rsFastLime, rsKame, Dreiklang, mGeos-M, EYQ1, KFP1, rsCherry, rsCherryRev, rsTagRFP, mApple, asFP595, Kindling FP, rseGFP, and rseGFP2 in order to detect the desired sample.
Claims 16-18 are rejected under 35 U.S.C. 103 as being unpatentable over Lombana as applied to claim 1 above, and further in view of Kastrup (US 2023/0120931 A1).
Regarding claim 16, Lombana is silent regarding wherein the one or more taggable markers comprise a phototransformable dye.
However, Kastrup teaches sample imaging (abstract) wherein the one or more taggable markers comprise a phototransformable dye (paragraphs [0019]-[0023]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Kastrup by including wherein the one or more taggable markers comprise a phototransformable dye in order to produce a high resolution image of the sample.
Regarding claim 17, Lombana is silent regarding wherein the phototransformable dye is a photoactivatable dye.
However, Kastrup teaches sample imaging (abstract) wherein the phototransformable dye is a photoactivatable dye (paragraphs [0019]-[0023]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Kastrup by including wherein the phototransformable dye is a photoactivatable dye in order to produce a high resolution image of the sample..
Regarding claim 18, Lombana is silent regarding wherein the phototransformable dye is selected from the group consisting of: PA-JF549, PA-JF646, DCDHF-based dyes, and BODIPY-based dyes.
However, Kastrup teaches sample imaging (abstract) wherein the phototransformable dye is selected from the group consisting of: PA-JF549, PA-JF646, DCDHF-based dyes, and BODIPY-based dyes (paragraphs [0023]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Kastrup by including wherein the phototransformable dye is selected from the group consisting of: PA-JF549, PA-JF646, DCDHF-based dyes, and BODIPY-based dyes in order to use a single light source.
Claims 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over Lombana as applied to claim 1 above, and further in view of Osseiran, Sam, et al. "Longitudinal monitoring of cancer cell subpopulations in monolayers, 3D spheroids, and xenografts using the photoconvertible dye DiR." Scientific Reports 9.1 (2019): 5713, hereinafter “Osseiran”.
Regarding claim 19, Lombana is silent regarding wherein the phototransformable dye is a photoconvertible dye.
However, Osseiran teaches optical analysis of a sample (abstract) including wherein the phototransformable dye is a photoconvertible dye (page 2, paragraphs 2-5).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Osseiran by including wherein the phototransformable dye is a photoconvertible dye in order to map the chosen sample. 
Regarding claim 20, Lombana is silent regarding wherein the photoconvertible dye is a DiR-based photoconvertible dye.
However, Osseiran teaches optical analysis of a sample (abstract) including wherein the photoconvertible dye is a DiR-based photoconvertible dye (page 2, paragraphs 2-5).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Osseiran by including wherein the photoconvertible dye is a DiR-based photoconvertible dye in order to map the chosen sample. 
Claims 21-22 are rejected under 35 U.S.C. 103 as being unpatentable over Lombana as applied to claim 1 above, and further in view of Kastrup (US 2024/0060121 A1).
Regarding claim 21, Lombana is silent regarding wherein the phototransformable dye is a photoswitchable dye.
However, Kastrup teaches optical analysis of a sample (abstract) including wherein the phototransformable dye is a photoswitchable dye (paragraph [0136]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Kastrup by including wherein the photoconvertible dye is a DiR-based photoconvertible dye in order to map the chosen sample. 
Regarding claim 22, Lombana is silent regarding wherein the photoswitchable dye is selected from the group consisting of: Atto 488, Cy3B, Alexa 647, Cy7, Alexa 750, and Si-Rhodamine dyes.
However, Kastrup teaches optical analysis of a sample (abstract) including wherein the photoswitchable dye is selected from the group consisting of: Atto 488, Cy3B, Alexa 647, Cy7, Alexa 750, and Si-Rhodamine dyes (paragraph [0136]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to combine the method of Lombana with the teaching of Kastrup by including wherein the photoswitchable dye is selected from the group consisting of: Atto 488, Cy3B, Alexa 647, Cy7, Alexa 750, and Si-Rhodamine dyes in order to map the chosen sample. 
Allowable Subject Matter
Claims 5-7 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The following is a statement of reasons for the indication of allowable subject matter:
Regarding claim 5, the prior art of record, taken either alone or in combination, fails to disclose or render obvious a method for screening cellular, subcellular or multicellular structures, the method comprising, among other essential elements, wherein the one or more structures of the plurality further comprise one or more selectable markers; the one or more phototransformed taggable markers within the target structure cause the activation of one or more selectable markers within the target structure to produce one or more activated selectable markers; isolating the one or more tagged target structures is performed by culturing the plurality of structures in an environment only amenable to structures comprising the one or more activated selectable markers to produce one or more isolated tagged target structures, in combination with the rest of the limitations of claim 1 and the above claim.  Claims 6-7 are dependent from claim 5 and therefore are also included in the allowed subject matter.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Lavis (US 11958976 B2) teaches photoactive in vivo labeling of proteins, but does not teach the above limitations.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DOMINIC J BOLOGNA whose telephone number is (571)272-9282. The examiner can normally be reached Monday - Friday 7:30am-3:30pm.
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/DOMINIC J BOLOGNA/Primary Examiner, Art Unit 2877