In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

A system for automated microorganism identification and antibiotic susceptibility testing comprising a reagent cartridge, a reagent stage, a cassette, a cassette, stage, a pipettor assembly, an optical detection system, and a controller is disclosed. The system is designed to dynamically adjust motor idle torque to control heat load and employs a fast focus process for determining the true focus position of an individual microorganism. The system also may quantify the relative abundance of viable microorganisms in a sample using dynamic dilution, and facilitate growth of microorganisms in customized media for rapid, accurate antimicrobial susceptibility testing.

In biosciences and related fields, it can be useful to study cells in isolation so that cells having unique and desirable properties can be identified within a heterogenous mixture of cells. Processes and methods disclosed herein provide for encapsulating cells within a microfluidic device and assaying the encapsulated cells. Encapsulation can, among other benefits, facilitate analyses of cells that generate secretions of interest which would otherwise rapidly diffuse away or mix with the secretions of other cells.

A system and method for target material retrieval and processing, the system comprising: an adaptor configured to interface with a capture region of a capture substrate for capturing particles in single-particle format within a set of wells, wherein the adaptor comprises a first region configured to interface with the capture region, a second region, and a cavity extending from the first region to the second region; and a support structure coupled to the adaptor and providing a set of operation modes for movement of the adaptor relative to the capture substrate. The system enables methods for magnetic and/or other force-based methods of retrieval of target material (e.g., derived from single cells).

Disclosed herein are cellular cassettes for the storage, collection, and analysis of biological samples. The cellular cassette can enable easy sample collection and sealing of microwell arrays with semi-permeable membrane for stable storage and future processing of single cells. Also disclosed herein are systems and kits comprising one or more described cassettes. The described cassettes, systems, and kits can be used to create barcoded, single-cell sequencing libraries. Further described herein are methods of using the cassettes, systems, and kits.

The present invention is directed to sample test cards having an increased sample well capacity for analyzing biological or other test samples. In one embodiment, the sample test cards of the present invention comprise one or more fluid over-flow reservoirs, wherein the over-flow reservoirs are operatively connected to a distribution channel by a fluid over-flow channel. In another embodiment, the sample test cards may comprise a plurality of flow reservoirs operable to trap air thereby reducing and/or preventing well-to-well contamination. The test card of this invention may comprise from 80 to 140 individual sample wells, for example, in a test card sample test cards of the present invention have a generally rectangular shape sample test card having dimensions of from about 90 to about 95 mm in width, from about 55 to about 60 mm in height and from about 4 to about 5 mm in thickness.

Described herein are systems and methods which utilize an array of wells to isolate pathogens and nucleic acid detection techniques to accurately and rapidly detect pathogens in fluid samples, even in very low concentrations, including from solid or semi-solid samples that have been fluidized. The provided systems and methods dry the fluid sample to deposit a fraction of the total volume in a number of wells and perform nucleic acid detection on individual wells to detect even individual pathogens and provide a quantitative analysis of the amount of pathogen within the sample. Also provided are methods and systems for precise delivery of dried materials, including biomolecules that are enzymes of use in the process, to microwells.

The present disclosure relates to an analytical system with at least three components: a multiwell plate on which the wells are included in an optically transparent area; a frame holding the multiwell plate close to its edge while permitting the plate a certain extent of freedom of movement; a baseplate to which the multiwell plate, but not the frame is firmly fixed via a docking mechanism, such that different expansion of plate and frame can be compensated. A second aspect described herein relates to a method of docking a corresponding multiwell plate held by a frame to a baseplate and subjecting the multiwell plate to a step of a biological or chemical assay within this arrangement.

An improved system, method and interface for automated rapid antimicrobial susceptibility testing (AST) is disclosed which includes, in one aspect, a carrier population station comprising a workstation having a graphic user interface (GUI). The GUI accepts information from a lab technologist, including information related to a scope of testing to be performed on a microorganism containing sample. The GUI controls intelligent assignment of microorganism containing samples to test panels in a manner that maximize utilization of the test carrier by grouping together samples of similar tests scopes and advantageously testing those samples using one multiplexed test panel. Customizing workflow in accordance with test scope to facilitate parallel processing of multiple samples advantageously reduces laboratory waste, decreases test latencies, increases AST system throughput and efficiency, and thus lowers the costs to the AST lab.

A microfluidic apparatus and methods thereof. The Apparatus having a flat and thin substrate, the substrate including at least one microfluidic testing device, each device with: plurality of Stationary Nanoliter Droplet Array (SNDA) components; a common inlet port and a distribution manifold, configured to enable an introduction of a fluid into all the primary channels; plurality of individual inlet ports, each coupled to a different primary channel, configured to enable an individual introduction of a fluid into its associated primary channel; and one or more outlet ports and optionally a collecting manifold, configured to evacuate liquid and/or gas flowing out thereof.