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 Objections
Claim 28 is objected to because of the following informalities: In claim 28, Examiner suggests correction of “obtaining a image” to read as “obtaining an image”. Appropriate correction is required.
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.
Claims 28, 32, 34 and 42-47 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by “Pluri-IQ: Quantification of Embryonic Stem Cell Pluripotency through an Image-Based Analysis Software” (hereinafter “Perestrelo”; published 2017).
Regarding claim 28, Perestrelo discloses a method for characterizing pluripotency of a plurality of cells, the method comprising (Perestrelo, Fig. 2):
obtaining a image of the plurality of cells (Perestrelo, p.698, Results section, Fig. 2; “These mESCs were cultured in different medium conditions that promote maintenance of pluripotency or induce mESC differentiation. Cells were stained with AP. Subsequently, low magnification phase-contrast images and a fluorescence channel for AP staining were acquired.”);
applying, to the image, a predictive model comprising a pluripotency model and a cell localization model, the pluripotency model configured to translate the image to an intermediate mask representation comprising pluripotency predictions of biomarker intensities for the plurality of cells in the image, and the cell localization model configured to identify locations of the plurality of cells within the image (Perestrelo, p.698, left column, last paragraph, Fig. 2; “we present an accurate, open-source, and user-friendly software, Pluri-IQ, which can automatically quantify the percentage of pluripotent, mixed, or differentiated cells through culture images. Pluri-IQ is able to analyze different low-magnification image sizes, and through core cascade modules (segmentation, machine learning, validation, and automatic scoring) accurately quantifies pluripotency” wherein “Pluri-IQ segments both phase-contrast image channel to get all colonies, and the pluripotent marker channel”, the results of segmentation of cell colonies and pluripotent cell colonies based on marker intensity are shown in the “Segmentation” column of Fig. 2); and
generating at least pluripotency metrics for the plurality of cells according to the intermediate mask representation and using the identified locations of the plurality of cells predicted by the cell localization model, the pluripotency metrics indicative of pluripotency of the plurality of cells (Perestrelo, p.698, left column, last paragraph – p.700, left column, Fig. 2, Fig. 3; “we present an accurate, open-source, and user-friendly software, Pluri-IQ, which can automatically quantify the percentage of pluripotent, mixed, or differentiated cells through culture images. Pluri-IQ is able to analyze different low-magnification image sizes, and through core cascade modules (segmentation, machine learning, validation, and automatic scoring) accurately quantifies pluripotency” wherein “After colony segmentation is completed, all colonies detected are assigned with a specific number (ID), with the colony ID derived from the phase-contrast image applied to the pluripotent marker image”, and the automatic score is based on the combined colony segmentation and pluripotent marker segmented images).
Regarding claim 32, claim 28 is incorporated, and Perestrelo further discloses wherein the biomarker intensities comprise intensities of biomarkers selected from any of Oct4, Sox2, Klf4, c-Myc, Nanog,Lin28, SSEA-4, Tra-1-60, Tra-1-81, Alkaline Phosphatase, CD9, E-cadherin, and PODXL (Perestrelo, p.697-698, Introduction and Results Sections; “These mESCs were cultured in different medium conditions that promote maintenance of pluripotency or induce mESC differentiation. Cells were stained with AP. Subsequently, low magnification phase-contrast images and a fluorescence channel for AP staining were acquired.” AP is alkaline phosphatase; therefore, the selection requirement of the claim is met.).
Regarding claim 34, claim 28 is incorporated, and Perestrelo further discloses wherein the intermediate mask representation shares a same image resolution as the image (Perestrelo, Fig. 2, the same image is processed to obtain both the pluripotent marker segmentation image mask and the colony segmentation image mask).
Regarding claim 42, claim 28 is incorporated, and Perestrelo further discloses wherein the predictive model is trained with paired images and immunofluorescent images (Perestrelo, p.701, left column; “After selecting the colonies, the classifier is built taking into account different colony features from both phase contrast and pluripotent marker images”).
Regarding claim 43, claim 28 is incorporated, and Perestrelo further discloses wherein obtaining the image of the plurality of cells comprises: culturing the plurality of cells; and capturing the image of the plurality of cells (Perestrelo, p.697-698, Introduction and Results Sections; “These mESCs were cultured in different medium conditions that promote maintenance of pluripotency or induce mESC differentiation. Cells were stained with AP. Subsequently, low magnification phase-contrast images and a fluorescence channel for AP staining were acquired.”).
Regarding claim 44, claim 43 is incorporated, and Perestrelo further discloses wherein the plurality of cells are cultured in vitro or ex vivo (Perestrelo, p.697-698, Introduction and Results Sections; “These mESCs were cultured in different medium conditions that promote maintenance of pluripotency or induce mESC differentiation. Cells were stained with AP. Subsequently, low magnification phase-contrast images and a fluorescence channel for AP staining were acquired.”).
Regarding claim 45, claim 28 is incorporated, and Perestrelo further discloses wherein the plurality of cells are selected from any of induced pluripotent cells (iPSCs), embryonic stem cells, or cells derived from germ layers (Perestrelo, p.697-698, Introduction and Results Sections; “To evaluate the performance of Pluri-IQ, we tested its classification precision over a set of mESCs images” – mESCs satisfy the requirement that the cells may be selected to be embryonic stem cells).
Regarding claim 46, claim 28 is incorporated, and Perestrelo further discloses wherein the image is any of a bright-field image, phase-contrast image, dark-field image, Reinberg Illumination image, or polarization image (Perestrelo, p.697-698, Introduction and Results Sections; “low magnification phase-contrast images and a fluorescence channel for AP staining were acquired.”).
Regarding claim 47, claim 28 is incorporated, and Perestrelo further discloses wherein the image is captured using optical microscopy (Perestrelo, p.708, Imaging Acquistion; “All images were collected with a Nikon DS-QiMc camera installed on a customized Nikon TE300 epifluorescent microscope”).
Claim Rejections - 35 USC § 103
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.
Claims 29-31 are rejected under 35 U.S.C. 103 as being unpatentable over Perestrelo, as applied to claim 28 above, in view of “Chemical ablation of tumor-initiating human pluripotent stem cells” (hereinafter “Ben-David”; applicant-submitted prior art, published 2014).
Regarding claim 29, claim 28 is incorporated, and Perestrelo does not expressly teach the limitations as further claimed, but, in an analogous field of endeavor, Ben-David does as follows.
Ben-David teaches identifying one or more cells from the plurality of cells based on the generated pluripotency metrics; and isolating the identified one or more cells from the plurality of cells (Ben-David, p.730, Fig. 1, "Advantages and limitations in comparison with other methods"; "methods for the removal of undifferentiated cells from culture" include separation of the cells from the culture).
Ben-David is considered analogous art because it pertains to pluripotent stem cell analysis. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date to the claimed invention to modify the method taught by Perestrelo to include further steps of using the differentiation state of the cells to identify undifferentiated cells to be removed from the cell culture, as taught by Ben-David, in order to enable isolation or separation of pluripotent cells from the culture (Ben-David, Introduction).
Regarding claim 30, claim 29 is incorporated, and Ben-David in the combination further teaches wherein isolating the one or more cells comprises ablating non-identified cells while maintaining the identified one or more cells (Ben-David, p.729, "Chemical ablation of hPSCs", Fig. 1, Fig. 2; "The simple chemical protocol presented here can be easily applied without specialist equipment for fast, robust and inexpensive elimination of undifferentiated hPSCs from culture.").
Regarding claim 31, claim 30 is incorporated, and Ben-David in the combination further teaches wherein isolating the one or more cells comprises: physically removing the isolated one or more cells from the plurality of cells; and culturing the physically removed isolated one or more cells (Ben-David, p.729, Introduction, p.730, Fig. 1, Fig. 2, "Advantages and limitations in comparison with other methods"; "methods for the removal of undifferentiated cells from culture" include separation of the undifferentiated cells from the cell culture).
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Perestrelo, as applied to claim 28 above, in view of US PG PUB. 2020/0224172 A1 (hereinafter “Shiebinger”; applicant-submitted prior art).
Regarding claim 33, claim 28 is incorporated, and Perestrelo does not expressly teach the limitations as further claimed, but, in an analogous field of endeavor, Shiebinger does as follows.
Shiebinger teaches wherein the predictive model is trained using one or more images indicative of expression profiles of one or more genes correlated to cellular pluripotency determined via RNA fluorescent in situ hybridization (RNA-FISH) or sequential fluorescence in situ hybridization (SeqFISH+) (Schiebinger, ¶0240, 0325; "recent study (60) reported that X-reactivation follows the activation of various pluripotency genes, based on immunofluorescence and RNA FISH in single cells. To assess X-reactivation, from scRNA-Seq data, each cell was characterized with respect to signatures of X-inactivation (Xist expression), X-reactivation (proportion of transcripts derived from X-linked genes, normalized to cells at day 0), and early and late pluripotency genes.").
Schiebinger is considered analogous art because it pertains to biological cell image analysis. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the training images in Perestrelo to include immunofluorescence images representing biomarkers signatures indicative of genetic expression linked to pluripotency, as taught by Schiebinger, in order to more accurately determine the state of differentiation in pluripotent stem cells using the neural network trained on these images (Nelson, ¶0019-0021).
Claims 35-37 are rejected under 35 U.S.C. 103 as being unpatentable over Perestrelo, as applied to claim 28 above, in view of “A Machine Learning Assisted, Label-free, Non-invasive Approach for Somatic Reprogramming in Induced Pluripotent Stem Cell Colony Formation Detection and Prediction” (hereinafter “Fan”; applicant-submitted prior art, published 2017).
Regarding claim 35, claim 28 is incorporated, and Perestrelo does not expressly teach the limitations as further claimed, but, in an analogous field of endeavor, Fan does as follows.
Fan teaches wherein the pluripotency model is a neural network (Fan, Fig. 1, Fig. 4, p.2, last paragraph before Results – p.7; “This automated system involves a computer vision recognition model to assist in the classification of iPSC colonies from bright-field microscopic images. This model utilizes a convolution neural network as a classifier in a sliding windows framework for colony recognition”).
Fan is considered analogous art because it pertains to pluripotent stem cell analysis based on microscopy images. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method taught by Perestrelo to implement a neural network as the pluripotency classifier, as taught by Fan, in order to accurately detect pluripotent stem cell colonies (Fan, pgs. 6-7, Methods).
Regarding claim 36, claim 35 is incorporated, and Fan in the combination further teaches wherein the neural network comprises a plurality of layers (Fan, p.8, Neural Network Design and Iterative training; “A batch-normalized layer was added before each convolution layer to accelerate the training speed and slightly improve the performance.”).
Regarding claim 37, claim 28 is incorporated, and Perestrelo does not expressly teach the limitations as further claimed, but, in an analogous field of endeavor, Fan does as follows.
Fan teaches wherein the pluripotency model comprises one or more downsampling operators or one or more upsampling operators (Fan, p.8, Neural Network Design and Iterative training; “We used a modified AlexNet32 structure as the base of our neural network design.”).
Fan is considered analogous art because it pertains to pluripotent stem cell analysis based on microscopy images. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method taught by Perestrelo to implement a neural network as the pluripotency classifier, as taught by Fan, in order to accurately detect pluripotent stem cell colonies (Fan, pgs. 6-7, Methods).
Claim 38 is rejected under 35 U.S.C. 103 as being unpatentable over Perestrelo, as applied to claim 28 above, in view of “Fully Convolutional Networks for Semantic Segmentation” (hereinafter “Long”; applicant-submitted prior art, published 2015).
Regarding claim 38, claim 28 is incorporated, and Perestrelo does not expressly teach the limitations as further claimed, but, in an analogous field of endeavor, Long does as follows.
Long teaches wherein the pluripotency model comprises one or more skip connections (Long, Abstract, Introduction and Section 4; “Next, we add skips between layers to fuse coarse, semantic and local, appearance information.”).
Long is considered analogous art because it pertains to image segmentation. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method taught by Perestrelo to implement the pluripotency marker segmentation using a neural network with skips between layers, as taught by Long, in order to refine the semantics and spatial precision of the segmentation output (Long, Section 4).
Claims 39-40 are rejected under 35 U.S.C. 103 as being unpatentable over Perestrelo, as applied to claim 28 above, in view of “Induced Pluripotent Stem Cells Recognition and Localization” (hereinafter “Wang”; published 2019).
Regarding claim 39, claim 28 is incorporated, and Perestrelo does not expressly teach the limitations as further claimed, but, in an analogous field of endeavor, Wang does as follows.
Wang teaches wherein the cell localization model is a neural network (Wang, p.1128, Section 4 Cell Recognition based on Faster RCNN+Alexnet – p.1131, Section 6 Conclusions, Figs. 16-17; “In order to realize the automatic identification, localization and picking of induced pluripotent stem cells, this paper proposes a cell recognition and localization method based on deep learning recognition location classification…Firstly, the training parameters of the Faster RCNN are adjusted several times to determine the optimal model training parameters…After that, the cell area is traversed and classified by training the Alexnet network. More precise cell area coordinates are obtained, and then the image of the culture dish area is spliced by a splicing algorithm combining Fourier transform and least squares method, and finally the spliced image is manipulated to obtain the final cell area coordinates. The above method can basically realize the recognition and localization of the induced pluripotent stem cells”).
Wang is considered analogous art because it pertains to pluripotent stem cell localization in microscopy images. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method taught by Perestrelo to implement the cell colony segmentation using a neural network, as taught by Wang, in order to obtain more precise cell area coordinates of pluripotent cells in the image (Wang, p.1131, Conclusions).
Regarding claim 40, claim 39 is incorporated, and Wang in the combination further teaches wherein the cell localization model generates bounding box localizations for each cell of at least a subset of the plurality of cells (Wang, p.1131, Section 5.2 - Section 6 Conclusions, Fig. 17; “the circumscribed rectangle coordinates of the region are obtained, and a rectangular frame is drawn on the original image, and the final result is obtained”).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 28 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,045,982. Although the claims at issue are not identical, they are not patentably distinct from each other because, aside from minor differences in claim language, claim 28 of the instant application is anticipated by claim 1 of the patent, as shown in the table below (differences underlined for emphasis).
Claim 28 of the Instant Application
Claim 1 of the Patent
28. A method for characterizing pluripotency of a plurality of cells, the method comprising:
obtaining a image of the plurality of cells;
applying, to the image, a predictive model comprising a pluripotency model and a cell localization model, the pluripotency model configured to translate the image to an intermediate mask representation comprising pluripotency predictions of biomarker intensities for the plurality of cells in the image, and the cell localization model configured to identify locations of the plurality of cells within the image; and
generating at least pluripotency metrics for the plurality of cells according to the intermediate mask representation and using the identified locations of the plurality of cells predicted by the cell localization model, the pluripotency metrics indicative of pluripotency of the plurality of cells.
1. A method for characterizing pluripotency of a plurality of cells, the method comprising:
obtaining a contrast image of the plurality of cells;
applying, to the contrast image, a predictive model comprising a pluripotency model comprising one or more skip connections and a cell localization model, the pluripotency model configured to translate the contrast image to an intermediate mask representation comprising pluripotency predictions of biomarker intensities for the plurality of cells in the contrast image, and the cell localization model configured to identify locations of the plurality of cells within the contrast image; and
generating at least pluripotency metrics for the plurality of cells according to the intermediate mask representation and using the identified locations of the plurality of cells predicted by the cell localization model, the pluripotency metrics indicative of pluripotency of the plurality of cells.
Claim 32 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 2 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 33 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 3 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 34 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 4 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 35 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 5 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 37 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 6 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 38 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 39 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 7 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 40 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 8 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 41 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 9 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 42 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 10 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 43 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 11 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 44 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 12 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 45 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 13 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 46 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 14 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Claim 47 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 15 of U.S. Patent No. 12,045,982 for the same rationale as applied to claim 28.
Allowable Subject Matter
Claim 41 is 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: None of the prior art of record, either alone or in combination, expressly teaches the limitation “wherein generating pluripotency metrics for the plurality of cells further comprises: for a cell at an identified location predicted by the cell localization model: determining a proportion of pixels in the intermediate mask representation at the identified location with a value that is indicative of the cell being pluripotent.” Perestrelo at most discloses generating a percent pluripotency of each colony or percent area of pluripotent colonies in the image, but does not expressly disclose or suggest this particular method of determining a pluripotency metric for an individual cell at a an identified location.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. The additionally provided references pertain generally to pluripotent cell recognition and image processing.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAMAH A BEG whose telephone number is (571)270-7912. The examiner can normally be reached M-F 9 AM - 5 PM.
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/SAMAH A BEG/Primary Examiner, Art Unit 2676
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