A method for optically detecting mutations in a sequence of DNA is disclosed. The method includes generating an optically coded input sequence by optically coding an input sequence, generating an optically coded reference sequence by optically coding a reference sequence, generating an aligned sequence by overlapping the optically coded input sequence with the optically coded reference sequence, and determining a mutation in the input sequence with respect to the reference sequence. The input sequence includes an input arrangement of a plurality of elements. Each of the plurality of elements includes an element value of a plurality of element values. The reference sequence includes a reference arrangement of the plurality of elements. Each element of the aligned sequence includes one of a low-value element or a high-value element. The mutation is determined responsive to detecting the low-value element in the aligned sequence.

Disclosed are a super-resolution imaging system (1, 41, 51), a super-resolution imaging method, a biological sample identification system (4, 61) and method, a nucleic acid sequencing imaging system (5) and method, and a nucleic acid identification system (6) and method. The super-resolution imaging system (1, 41, 51) includes an illumination system (A) and an imaging system (B). The illumination system (A) outputs excitation light to irradiate a biological sample to generate excited light, and the imaging system (B) collects and records the excited light to generate an excited light image. The illumination system (A) includes an excitation light source (10, 10a) and a structured light generation and modulation device (11, 11a). The excitation light source (10, 10a) outputs the excitation light, and the structured light generation and modulation device (11, 11a) modulates the excitation light into structured light to irradiate the biological sample to generate the excited light.

Disclosed are a super-resolution imaging system (1, 41, 51), a super-resolution imaging method, a biological sample identification system (4, 61) and method, a nucleic acid sequencing imaging system (5) and method, and a nucleic acid identification system (6) and method. The super-resolution imaging system (1, 41, 51) includes an illumination system (A) and an imaging system (B). The illumination system (A) outputs excitation light to irradiate a biological sample to generate excited light, and the imaging system (B) collects and records the excited light to generate an excited light image. The illumination system (A) includes an excitation light source (10, 10a) and a structured light generation and modulation device (11, 11a). The excitation light source (10, 10a) outputs the excitation light, and the structured light generation and modulation device (11, 11a) modulates the excitation light into structured light to irradiate the biological sample to generate the excited light.

A system for determining the number of target nucleotide molecules in a sample includes a sample holder, an excitation optical system, an optical sensor, and an emission optical system. The sample holder is configured to receive an article comprising at least 20,000 separate reaction sites. The excitation optical system comprises a light source configured to simultaneously illuminate the at least 20,000 separate reaction sites. The optical sensor comprises a predetermined number of pixels, the predetermined number of pixels being at least 20 times the number of separate reaction sites. The emission optical system comprises a system working distance from the sample holder, wherein the working distance is less than or equal to 60 millimeters.

A system for determining the number of target nucleotide molecules in a sample includes a sample holder, an excitation optical system, an optical sensor, and an emission optical system. The sample holder is configured to receive an article comprising at least 20,000 separate reaction sites. The excitation optical system comprises a light source configured to simultaneously illuminate the at least 20,000 separate reaction sites. The optical sensor comprises a predetermined number of pixels, the predetermined number of pixels being at least 20 times the number of separate reaction sites. The emission optical system comprises a system working distance from the sample holder, wherein the working distance is less than or equal to 60 millimeters.

A system for determining the number of target nucleotide molecules in a sample includes a sample holder, an excitation optical system, an optical sensor, and an emission optical system. The sample holder is configured to receive an article comprising at least 20,000 separate reaction sites. The excitation optical system comprises a light source configured to simultaneously illuminate the at least 20,000 separate reaction sites. The optical sensor comprises a predetermined number of pixels, the predetermined number of pixels being at least 20 times the number of separate reaction sites. The emission optical system comprises a system working distance from the sample holder, wherein the working distance is less than or equal to 60 millimeters.

A system for determining the number of target nucleotide molecules in a sample includes a sample holder, an excitation optical system, an optical sensor, and an emission optical system. The sample holder is configured to receive an article comprising at least 20,000 separate reaction sites. The excitation optical system comprises a light source configured to simultaneously illuminate the at least 20,000 separate reaction sites. The optical sensor comprises a predetermined number of pixels, the predetermined number of pixels being at least 20 times the number of separate reaction sites. The emission optical system comprises a system working distance from the sample holder, wherein the working distance is less than or equal to 60 millimeters.

The present invention concerns a microfluidic device or chip including at least one inlet for introducing at least one object into the device; an oil inlet for introducing an oil that supports droplet formation into the device or a droplet forming substance inlet for introducing a droplet forming substance into the device; a co-encapsulation area or structure where the at least one object is encapsulated by the droplet; a microfluidic tubing or channel for transporting the at least one object to an entrance of the co-encapsulation area or structure; an oil supporting droplet formation microchannel or droplet forming substance microchannel connected to the microfluidic tubing or channel to place a liquid of the microfluidic tubing or channel in direct contact with the oil that supports droplet formation or the droplet forming substance; and a droplet microchannel or tubing for transporting the droplet.

The present invention concerns a microfluidic device or chip including at least one inlet for introducing at least one object into the device; an oil inlet for introducing an oil that supports droplet formation into the device or a droplet forming substance inlet for introducing a droplet forming substance into the device; a co-encapsulation area or structure where the at least one object is encapsulated by the droplet; a microfluidic tubing or channel for transporting the at least one object to an entrance of the co-encapsulation area or structure; an oil supporting droplet formation microchannel or droplet forming substance microchannel connected to the microfluidic tubing or channel to place a liquid of the microfluidic tubing or channel in direct contact with the oil that supports droplet formation or the droplet forming substance; and a droplet microchannel or tubing for transporting the droplet.

This invention relates to systems and methods for imaging sample materials within a microfluidic device during an assay reaction process. In accordance with certain aspects of the invention, images are formed with a pixel array and a region of interest (ROI) is defined within the pixel array. Image values, such as fluorescent intensity, can be computed as averages of individual pixel values within the ROI. Where the ROI is subject to non-uniform conditions, such as non-uniform heating, the ROI can be divided into sub-ROIs which are sufficiently small that the condition is uniform within the sub-ROI.