Abstract: A sequencing instrument including a sequencing stage and a microscope. The sequencing stage has a reference plate with a flat reference surface. The microscope optical axis is perpendicular to the reference surface. The sequencing stage is configured to receive a flexible film having a plurality of DNA templates immobilized on a first side of the film, and to hold the flexible film against the flat reference surface with at least some of the plurality of DNA templates in an object plane that is perpendicular to the microscope's optical axis.

Abstract: A flowcell for a sequencing instrument. The flowcell includes a fluid inlet, a fluid outlet, a flow channel formed between an at least partially transparent cover and a base and fluidly connecting the fluid inlet to the fluid outlet, and a capture substrate provided in the flow channel. The capture substrate includes microretainers configured to each receive a single microspot having a microspot diameter, and microretainer is separated from adjacent microretainers by an interstitial gap distance that is equal to or greater than the microspot diameter. A particle separator may be fluidly connected to the flowcell. The particle separator may include a microfluidic channel having an array of micropillars to transfer a plurality of the microspots to a loading buffer that may be delivered to the flowcell.

Abstract: A processing instrument flowcell having a flowcell channel with an upstream channel end, a downstream channel end, a longitudinal axis extending from the upstream channel end to the downstream channel end, and a first operative surface extending between the upstream channel end and the downstream channel end and configured to receive a first number of DNA templates. A first reagent inlet is fluidically connected to the upstream channel end at a location adjacent the first operative surface. A buffer inlet is fluidically connected to the upstream channel end at a location spaced from the first operative surface. An outlet fluidically connected to the downstream channel end. Also provided is a method for operating a flowcell channel under laminar flow conditions to maintain a first reagent adjacent a first operative surface and a buffer fluid spaced from the first operative surface. The flowcell channel may have multiple separate operative surfaces.

Abstract: A flowcell for a sequencing instrument. The flowcell includes a fluid inlet, a fluid outlet, a flow channel formed between an at least partially transparent cover and a base and fluidly connecting the fluid inlet to the fluid outlet, and a capture substrate provided in the flow channel. The capture substrate includes microretainers configured to each receive a single microspot having a microspot diameter, and microretainer is separated from adjacent microretainers by an interstitial gap distance that is equal to or greater than the microspot diameter. A particle separator may be fluidly connected to the flowcell. The particle separator may include a microfluidic channel having an array of micropillars to transfer a plurality of the microspots to a loading buffer that may be delivered to the flowcell.

Abstract: A sequencing instrument including a sequencing stage and a microscope. The sequencing stage has a reference plate with a flat reference surface. The microscope optical axis is perpendicular to the reference surface. The sequencing stage is configured to receive a flexible film having a plurality of DNA templates immobilized on a first side of the film, and to hold the flexible film against the flat reference surface with at least some of the plurality of DNA templates in an object plane that is perpendicular to the microscope's optical axis.