A device includes a plurality of imaging pixels in a spatial pattern with a formation of features disposed over the pixels. A first and a second feature of the formation of features are disposed over a first pixel. A first luminophore is disposed within or over the first feature. A second luminophore is disposed within or over the second feature. A structured illumination source is to direct at least a portion of first photons in an illumination pattern to the first feature at a first time, and to direct at least a portion of second photons in the illumination pattern to the second feature at a second time. The structured illumination source includes an illumination pattern generator having an illumination pattern generator actuator connected to the illumination pattern generator to cause the illumination pattern to translate or rotate relative to the formation of features.

A device includes a plurality of imaging pixels in a spatial pattern with a formation of features disposed over the pixels. A first and a second feature of the formation of features are disposed over a first pixel. A first luminophore is disposed within or over the first feature. A second luminophore is disposed within or over the second feature. A structured illumination source is to direct at least a portion of first photons in an illumination pattern to the first feature at a first time, and to direct at least a portion of second photons in the illumination pattern to the second feature at a second time. The structured illumination source includes an illumination pattern generator having an illumination pattern generator actuator connected to the illumination pattern generator to cause the illumination pattern to translate or rotate relative to the formation of features.

The present disclosure provides compositions, methods and systems for sequencing a template nucleic acid using a polymerase based, nucleic acid binding reaction involving examination of the interaction between a polymerase and template nucleic acid in the presence of one or more unlabeled nucleotides. The methods rely, in part, on identifying a base of a template nucleic acid during nucleic acid synthesis by controlling the sequencing reaction conditions. Template nucleic acid bases may be identified during an examination step followed by an optional incorporation step.

The present disclosure provides compositions, methods and systems for sequencing a template nucleic acid using a polymerase based, nucleic acid binding reaction involving examination of the interaction between a polymerase and template nucleic acid in the presence of one or more unlabeled nucleotides. The methods rely, in part, on identifying a base of a template nucleic acid during nucleic acid synthesis by controlling the sequencing reaction conditions. Template nucleic acid bases may be identified during an examination step followed by an optional incorporation step.

Systems and methods for detection of a signal from droplets of an emulsion. An exemplary system may comprise a fluid transporter having a tube with an open end for aspirating droplets, a singulator to arrange the droplets in single file and to space the single-file droplets from one another, and a detection channel in optical communication with a detector configured to detect a signal from droplets. In some embodiments, the singulator may have a channel junction at which a stream of droplets in single file is combined with a stream of spacing fluid, and a tapered spacing channel extending downstream from the channel junction toward the detection channel. In some embodiments, the fluid transporter may suck droplet-containing fluid and spacing fluid through the detection channel from respective sources. In some embodiments, droplets may be subjected to a disaggregation routine before they are passed through the detection channel.

Systems and methods for detection of a signal from droplets of an emulsion. An exemplary system may comprise a fluid transporter having a tube with an open end for aspirating droplets, a singulator to arrange the droplets in single file and to space the single-file droplets from one another, and a detection channel in optical communication with a detector configured to detect a signal from droplets. In some embodiments, the singulator may have a channel junction at which a stream of droplets in single file is combined with a stream of spacing fluid, and a tapered spacing channel extending downstream from the channel junction toward the detection channel. In some embodiments, the fluid transporter may suck droplet-containing fluid and spacing fluid through the detection channel from respective sources. In some embodiments, droplets may be subjected to a disaggregation routine before they are passed through the detection channel.

The present invention provides methods and compositions for detecting genomic sequences of interest in living cells. In particular, the present disclosure provides a split-enzyme system that works with guide RNAs and RNA-guided nucleases to produce detectable luminescent signals exclusively in the presence of targeted genomic sequences.

The present invention provides methods and compositions for detecting genomic sequences of interest in living cells. In particular, the present disclosure provides a split-enzyme system that works with guide RNAs and RNA-guided nucleases to produce detectable luminescent signals exclusively in the presence of targeted genomic sequences.

In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, for in situ spatial profiling of biological materials such as DNA, RNA and protein in cells, tissues, and organisms for investigating biology and for conducting biomarker/drug discovery and development, and for clinical pathology and diagnosis. In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, for spatially determining, visualizing or quantifying target biological materials comprising in situ staining of a biological sample with one or a plurality of probes that are labeled with light-emitting moieties that exhibit or are encoded with distinct luminescence lifetime (and, optionally, spectrum) characteristics; followed by time-resolved luminescence imaging, measurement and analysis.

In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, for in situ spatial profiling of biological materials such as DNA, RNA and protein in cells, tissues, and organisms for investigating biology and for conducting biomarker/drug discovery and development, and for clinical pathology and diagnosis. In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, for spatially determining, visualizing or quantifying target biological materials comprising in situ staining of a biological sample with one or a plurality of probes that are labeled with light-emitting moieties that exhibit or are encoded with distinct luminescence lifetime (and, optionally, spectrum) characteristics; followed by time-resolved luminescence imaging, measurement and analysis.