Patents by Inventor Ali Kabiri
Ali Kabiri has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11454758Abstract: Apparatus and methods for improving optical signal collection in an integrated device are described. A microdisk can be formed in an integrated device and increase collection and/or concentration of radiation incident on the microdisk and re-radiated by the microdisk. An example integrated device that can include a microdisk may be used for analyte detection and/or analysis. Such an integrated device may include a plurality of pixels, each having a reaction chamber for receiving a sample to be analyzed, an optical microdisk, and an optical sensor configured to detect optical emission from the reaction chamber. The microdisk can comprise a dielectric material having a first index of refraction that is embedded in one or more surrounding materials having one or more different refractive index values.Type: GrantFiled: August 7, 2020Date of Patent: September 27, 2022Assignee: Quantum-Si IncorporatedInventors: Ali Kabiri, Bing Shen, Gerard Schmid, James Beach, Kyle Preston, Sharath Hosali
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Patent number: 11428635Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits radiation; at least one element for directing the emission radiation in a particular direction; and a light path along which the emission radiation travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the integrated device. Each sensor may detect emission radiation from a sample in a respective sample well. The instrument includes an excitation light source for exciting the sample in each sample well.Type: GrantFiled: July 5, 2018Date of Patent: August 30, 2022Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Benjamin Cipriany, Jack Jewell, Lawrence C. West, Michael Ferrigno, Paul E. Glenn, Anthony Bellofiore
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Patent number: 11422092Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: GrantFiled: January 28, 2021Date of Patent: August 23, 2022Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Gerard Schmid, Keith G. Fife, James Beach, Jason W. Sickler, Lawrence C. West, Paul E. Glenn, Kyle Preston, Farshid Ghasemi, Benjamin Cipriany, Jeremy Lackey
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Publication number: 20220214279Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: ApplicationFiled: March 25, 2022Publication date: July 7, 2022Applicant: Quantum-Si IncorporatedInventors: JONATHAN M. ROTHBERG, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Benjamin Ciperiany, Jack Jewell, Lawrence C. West, Michael Ferrigno, Paul E. Glenn, Adam Ezra Cohen, Anthony Bellofiore
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Publication number: 20220170861Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: ApplicationFiled: February 18, 2022Publication date: June 2, 2022Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Benjamin Cipriany, Jack Jewell, Lawrence C. West, Michael Ferrigno, Paul E. Glenn, Adam Ezra Cohen, Anthony Bellofiore
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Publication number: 20220128456Abstract: Aspects of the present disclosure relate to methods and systems for increasing the number of samples that can be processed in parallel by an integrated device An integrated device is provided having at least two reaction chambers disposed above an active photodetection area of a single pixel, such that the pixel is sensitive to photons from each of the at least two reaction chambers. In some embodiments, an integrated device may have at least four or more reaction chambers per photodetector. Signals from multiple reaction chambers may be distinguished using any combination of multiplexing techniques including techniques for waveguide multiplexing, intensity multiplexing, and/or lifetime multiplexing. According to further aspects of the technology described herein, there is provided techniques for increasing the amount of sample that can be processed by a single device by reloading an integrated device repeated times to process an increased number of samples by a single device.Type: ApplicationFiled: October 22, 2021Publication date: April 28, 2022Inventors: Todd Rearick, Ali Kabiri, Gerard Schmid, Kyle Preston
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Publication number: 20220120685Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: ApplicationFiled: October 8, 2021Publication date: April 21, 2022Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Paul E. Glenn, Lawrence C. West, Benjamin Cipriany, Keith G. Fife
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Publication number: 20220113469Abstract: An integrated device and related instruments and systems for analyzing samples in parallel are described. The integrated device may include sample wells arranged on a surface of where individual sample wells are configured to receive a sample labeled with at least one fluorescent marker configured to emit emission light in response to excitation light. The integrated device may further include photodetectors positioned in a layer of the integrated device, where one or more photodetectors are positioned to receive a photon of emission light emitted from a sample well. The integrated device further includes one or more photonic structures positioned between the sample wells and the photodetectors, where the one or more photonic structures are configured to attenuate the excitation light relative to the emission light such that a signal generated by the one or more photodetectors indicates detection of photons of emission light.Type: ApplicationFiled: December 17, 2021Publication date: April 14, 2022Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Gerard Schmid, Alexander Gondarenko, James Beach, Kyle Preston, Farshid Ghasemi, Jeremy Lackey, Jack Jewell, Keith G. Fife, Ali Kabiri
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Publication number: 20220099575Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: ApplicationFiled: October 8, 2021Publication date: March 31, 2022Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Patent number: 11287382Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: GrantFiled: November 19, 2019Date of Patent: March 29, 2022Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Benjamin Cipriany, Jack Jewell, Lawrence C. West, Michael Ferrigno, Paul E. Glenn, Adam Ezra Cohen, Anthony Bellofiore
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Patent number: 11237326Abstract: An integrated device and related instruments and systems for analyzing samples in parallel are described. The integrated device may include sample wells arranged on a surface of where individual sample wells are configured to receive a sample labeled with at least one fluorescent marker configured to emit emission light in response to excitation light. The integrated device may further include photodetectors positioned in a layer of the integrated device, where one or more photodetectors are positioned to receive a photon of emission light emitted from a sample well. The integrated device further includes one or more photonic structures positioned between the sample wells and the photodetectors, where the one or more photonic structures are configured to attenuate the excitation light relative to the emission light such that a signal generated by the one or more photodetectors indicates detection of photons of emission light.Type: GrantFiled: July 23, 2018Date of Patent: February 1, 2022Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Gerard Schmid, Alexander Gondarenko, James Beach, Kyle Preston, Farshid Ghasemi, Jeremy Lackey, Jack Jewell, Keith G. Fife, Ali Kabiri
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Patent number: 11226290Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: GrantFiled: June 1, 2017Date of Patent: January 18, 2022Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Gerard Schmid, Keith G. Fife, James Beach, Jason W. Sickler, Lawrence C. West, Paul E. Glenn, Kyle Preston, Farshid Ghasemi, Benjamin Cipriany, Jeremy Lackey
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Publication number: 20220011486Abstract: Apparatus and methods relating to attenuating excitation radiation incident on a sensor in an integrated device that is used for sample analysis are described. At least one semiconductor film of a selected material and crystal morphology is located between a waveguide and a sensor in an integrated device that is formed on a substrate. Rejection ratios greater than 100 or more can be obtained for excitation and emission wavelengths that are 40 nm apart for a single layer of semiconductor material.Type: ApplicationFiled: September 23, 2021Publication date: January 13, 2022Applicant: Quantum-Si IncorporatedInventors: Michael Bellos, Faisal R. Ahmad, James Beach, Michael Coumans, Sharath Hosali, Ali Kabiri, Kyle Preston, Gerard Schmid, Bing Shen, Jonathan M. Rothberg
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Patent number: 11181477Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: GrantFiled: November 19, 2019Date of Patent: November 23, 2021Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Patent number: 11175227Abstract: Apparatus and methods for analyzing single molecules and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: GrantFiled: June 17, 2019Date of Patent: November 16, 2021Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Paul E. Glenn, Lawrence C. West, Benjamin Cipriany, Keith G. Fife
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Publication number: 20210310066Abstract: Apparatus and techniques for electrokinetic loading of samples of interest into sub-micron-scale reaction chambers are described. Embodiments include an integrated device and related apparatus for analyzing samples in parallel. The integrated device may include at least one reaction chamber formed through a surface of the integrated device and configured to receive a sample of interest, such as a molecule of nucleic acid. The integrated device may further include electrodes patterned adjacent to the reaction chamber that produce one or more electric fields that assist loading the sample into the reaction chamber. The apparatus may further include a sample reservoir having a fluid seal with the surface of the integrated device and configured to hold a suspension containing the samples.Type: ApplicationFiled: June 17, 2021Publication date: October 7, 2021Applicant: Quantum-Si IncorporatedInventors: Guojun Chen, Jeremy Lackey, Alexander Goryaynov, Gerard Schmid, Ali Kabiri, Jonathan M. Rothberg, Todd Rearick, Jonathan C. Schultz, Farshid Ghasemi, Keith G. Fife
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Publication number: 20210270740Abstract: Some aspects relate to an integrated circuit, comprising at least one photodetection region configured to generate charge carriers responsive to incident photons emitted from a sample, at least one charge storage region configured to receive the charge carriers from the photodetection region, and at least one controller configured to obtain information about the incident photons, the information comprising at least one member selected from the group comprising pulse duration and interpulse duration and at least one member selected from the group comprising wavelength information, luminescence lifetime information, and intensity information. In some embodiments, the information comprises at least three, four, and/or five members selected from the group comprising wavelength information, luminescence lifetime information, intensity information, pulse duration information, and interpulse duration information. In some embodiments, the information obtained may be used to identify the sample.Type: ApplicationFiled: March 2, 2021Publication date: September 2, 2021Inventors: Gerard Schmid, Dajiang Yang, Eric A.G. Webster, Xin Wang, Todd Rearick, Changhoon Choi, Ali Kabiri, Kyle Preston, Brian Reed
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Patent number: 11072827Abstract: Apparatus and techniques for electrokinetic loading of samples of interest into sub-micron-scale reaction chambers are described. Embodiments include an integrated device and related apparatus for analyzing samples in parallel. The integrated device may include at least one reaction chamber formed through a surface of the integrated device and configured to receive a sample of interest, such as a molecule of nucleic acid. The integrated device may further include electrodes patterned adjacent to the reaction chamber that produce one or more electric fields that assist loading the sample into the reaction chamber. The apparatus may further include a sample reservoir having a fluid seal with the surface of the integrated device and configured to hold a suspension containing the samples.Type: GrantFiled: January 4, 2019Date of Patent: July 27, 2021Assignee: Quantum-Si IncorporatedInventors: Guojun Chen, Jeremy Lackey, Alexander Goryaynov, Gerard Schmid, Ali Kabiri, Jonathan M. Rothberg, Todd Rearick, Jonathan C. Schultz, Farshid Ghasemi, Keith G. Fife
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Publication number: 20210215605Abstract: Some aspects relate to integrated devices for obtaining timing and/or spectral information from incident light. In some embodiments, a pixel may include one or more charge storage regions configured to receive charge carriers generated responsive to incident photons from a light source, with charge carriers stored in the charge storage region(s) indicative of spectral and timing information. In some embodiments, a pixel may include regions having different depths, each configured to generate charge carriers responsive to incident photons. In some embodiments, a pixel may include multiple charge storage regions having different depths, and one or more of the charge storage regions may be configured to receive the incident photons and generate charge carriers therein. In some embodiments, a pixel may include an optical sorting element configured to direct at least some incident photons to one charge storage region and other incident photons to another charge storage region.Type: ApplicationFiled: January 14, 2021Publication date: July 15, 2021Inventors: Gerard Schmid, Dajiang Yang, Eric A.G. Webster, Xin Wang, Todd Rearick, Changhoon Choi, Ali Kabiri, Kyle Preston
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Publication number: 20210215606Abstract: Systems and methods for optical power distribution within an integrated device, in a substantially uniform manner, to a large number of sample wells and/or other photonic elements. The integrated device and related instruments and systems may be used to analyze samples in parallel. The integrated device may include a grating coupler configured to receive light from an excitation source and optically couple with multiple waveguides configured to couple with sample wells. Vertical extents of optical modes of individual waveguides may be modulated to adjust confinement of light within the waveguides. This modulation may enable more uniform distribution of excitation light to the sample wells, improve excitation efficiency, and prevent overpower on regions of the integrated device.Type: ApplicationFiled: January 14, 2021Publication date: July 15, 2021Applicant: Quantum-Si IncorporatedInventors: Gerard Schmid, Sharath Hosali, James Beach, Kyle Preston, Ali Kabiri, Bing Shen