Abstract: Methods and cartridges for detecting targets are provided. A biological sample is introduced to a cartridge. Targets in the sample are photonically labeled with fluorescent particles in a first liquid layer in the cassette. Photonically-labeled targets are separated out of the sample into a second liquid layer within the cassette, detected, and counted to show presence of the targets in the subject. Cartridges include a receiving reservoir, a mixing well for introducing the sample to photonic labels and magnetic particles, and an imaging well for detecting and counting targets from the sample. The sample may be a human stool sample. A filter may be used to filter particulates out of the sample.

Abstract: The invention provides analyzers that improve tests for detecting specific cellular, viral, and molecular targets in clinical, industrial, or environmental samples. The invention permits efficient and specific selection and sensitive imaging detection of individual microscopic targets at low magnification. Automated embodiments allow efficient walk-away, on-demand, random-access high-throughput testing. The analyzers perform tests without requiring wash steps thus streamlining engineering and lowering costs. Thus, the invention provides analyzers that can deliver rapid, accurate, and quantitative, easy-to-use, and cost-effective tests for analytes.

Abstract: The invention provides analyzers that improve tests for detecting specific cellular, viral, and molecular targets in clinical, industrial, or environmental samples. The invention permits efficient and specific selection and sensitive imaging detection of individual microscopic targets at low magnification. Automated embodiments allow efficient walk-away, on-demand, random-access high-throughput testing. The analyzers perform tests without requiring wash steps thus streamlining engineering and lowering costs. Thus, the invention provides analyzers that can deliver rapid, accurate, and quantitative, easy-to-use, and cost-effective tests for analytes.

Abstract: The disclosure provides cartridges that are pre-loaded with reagents for performing antimicrobial susceptibility testing (AST) and FISH testing. Cartridges of the disclosure include various incubation wells loaded with different antimicrobial agents for differential growth analysis. Imaging wells with species-specific microbial probes, fluorescent tags, magnetic particles and dye-cushion layers allow for tagging and imaging of target microbes for differential growth analysis.

Abstract: The invention provides systems and methods for rapid automated identification of microbes and antimicrobial susceptibility testing (AST) directly from a patient specimen, without specimen preparation. Specimens are loaded into an analytical cartridge for processing. Analytical cartridges are preloaded with species-specific labels that are used to identify and enumerate microbes in the specimen. Instruments, such as analyzers can be used to interact with analytical cartridges to carry out methods of the invention all within the cartridge.

Abstract: The invention provides devices that improve tests for detecting specific cellular, viral, and molecular targets in clinical, industrial, or environmental samples. The invention permits efficient detection of individual microscopic targets at low magnification for highly sensitive testing. The invention does not require washing steps and thus allows sensitive and specific detection while simplifying manual operation and lowering costs and complexity in automated operation. In short, the invention provides devices that can deliver rapid, accurate, and quantitative, easy-to-use, and cost-effective tests.

Abstract: The invention enables efficient, rapid, and sensitive enumeration of living cells by detecting microscopic colonies derived from in situ cell division using large area imaging. Microbial enumeration tests based on the invention address an important problem in clinical and industrial microbiology—the long time needed for detection in traditional tests—while retaining key advantages of the traditional methods based on microbial culture. Embodiments of the invention include non-destructive aseptic methods for detecting cellular microcolonies without labeling reagents. These methods allow for the generation of pure cultures which can be used for microbial identification and determination of antimicrobial resistance.

Abstract: The invention provides devices that improve tests for detecting specific cellular, viral, and molecular targets in clinical, industrial, or environmental samples. The invention permits efficient detection of individual microscopic targets at low magnification for highly sensitive testing. The invention does not require washing steps and thus allows sensitive and specific detection while simplifying manual operation and lowering costs and complexity in automated operation. In short, the invention provides devices that can deliver rapid, accurate, and quantitative, easy-to-use, and cost-effective tests.

Abstract: The invention enables efficient, rapid, and sensitive enumeration of living cells by detecting microscopic colonies derived from in situ cell division using large area imaging. Microbial enumeration tests based on the invention address an important problem in clinical and industrial microbiology—the long time needed for detection in traditional tests—while retaining key advantages of the traditional methods based on microbial culture. Embodiments of the invention include non-destructive aseptic methods for detecting cellular microcolonies without labeling reagents. These methods allow for the generation of pure cultures which can be used for microbial identification and determination of antimicrobial resistance.

Abstract: The invention provides a version of fluorescent in situ hybridization (FISH) in which all the steps are performed at physiological temperatures, i.e., body temperature, to detect and identify pathogenic bacteria in clinical samples. Methods of the invention use species-specific fluorescent probes to label clinically important infectious bacteria. A sample such as a urine sample is loaded into a cartridge, fluorescently labeled, and imaged with a microscope. Labelled bacteria are pulled down onto an imaging surface and a dye cushion is used to keep unbound probes off of the imaging surface. A microscopic image of the surface shows whether and in what quantities the infectious bacteria are present in the clinical sample.

Abstract: The invention provides multi-function instruments for automatically and simultaneously carrying out a variety of tests including identification of targets in specimens and antimicrobial susceptibility testing thereof. Application-specific cartridges are pre-loaded with all required reagents and allow for tests to be performed in a single testing device with no specimen preparation to, for example, rapidly detect infections, identify infectious pathogens, and analyze their susceptibility to various antimicrobial agents. Instruments include various stations for carrying out test steps that can be randomly accessed in any order dictated by the computer-controlled instrument. A carousel stores and incubates cartridges and, with a mechanical conveyor arm, transfers the cartridges between the required stations to carry out the tests. A plurality of different tests may be performed on a plurality of targets within an instrument, and the plurality of targets may be disposed in a single cartridge.

Abstract: The invention provides devices that improve tests for detecting specific cellular, viral, and molecular targets in clinical, industrial, or environmental samples. The invention permits efficient detection of individual microscopic targets at low magnification for highly sensitive testing. The invention does not require washing steps and thus allows sensitive and specific detection while simplifying manual operation and lowering costs and complexity in automated operation. In short, the invention provides devices that can deliver rapid, accurate, and quantitative, easy-to-use, and cost-effective tests.

Abstract: Methods and cartridges for detecting targets are provided. A biological sample is introduced to a cartridge. Targets in the sample are photonically labeled with fluorescent particles in a first liquid layer in the cassette. Photonically-labeled targets are separated out of the sample into a second liquid layer within the cassette, detected, and counted to show presence of the targets in the subject. Cartridges include a receiving reservoir, a mixing well for introducing the sample to photonic labels and magnetic particles, and an imaging well for detecting and counting targets from the sample. The sample may be a human stool sample. A filter may be used to filter particulates out of the sample.

Abstract: The invention provides devices that improve tests for detecting specific cellular, viral, and molecular targets in clinical, industrial, or environmental samples. The invention permits efficient detection of individual microscopic targets at low magnification for highly sensitive testing. The invention does not require washing steps and thus allows sensitive and specific detection while simplifying manual operation and lowering costs and complexity in automated operation. In short, the invention provides devices that can deliver rapid, accurate, and quantitative, easy-to-use, and cost-effective tests.

Abstract: The invention features methods for rapidly and sensitively identifying molecular targets in medical, industrial, and environmental samples. The invention labels target molecules and then images them using large area imaging. Diagnostic tests based on the invention can be rapid, ultrasensitive, quantitative, multiplexed, and automated. A broad range of infectious agents (e.g., bacteria, viruses, fungi, and parasites) and molecules (e.g., proteins, DNA, RNA, hormones, and drugs) can be detected by the methods. The invention enables rapid, ultra-sensitive, cost-effective, and portable assays. The ability of the invention to detect low levels of target molecules rapidly and cost-effectively results from the combination of high intensity labeling, formats that facilitate rapid reaction kinetics, and large area imaging based using either instrumentation made from off-the-shelf commercial components or no instrumentation at all.

Abstract: The invention provides an improved method for sensitive and specific detection of target molecules, cells, or viruses. The inventive method uses large area imaging to detect individual labeled targets complexed with a target-specific selection moiety. The invention eliminates wash steps through the use of target-specific selection through one or more liquid layers that can contain optical dye and density agents. By eliminating washes the invention simplifies instrumentation engineering and minimizes user steps and costs. The invention uses sensitive image analysis to enumerate individual targets in a large area, is scalable, and can be deployed in systems ranging in complexity from manual to highly automated.

Abstract: The invention enables efficient, rapid, and sensitive enumeration of living cells by detecting microscopic colonies derived from in situ cell division using large area imaging. Microbial enumeration tests based on the invention address an important problem in clinical and industrial microbiology—the long time needed for detection in traditional tests—while retaining key advantages of the traditional methods based on microbial culture. Embodiments of the invention include non-destructive aseptic methods for detecting cellular microcolonies without labeling reagents. These methods allow for the generation of pure cultures which can be used for microbial identification and determination of antimicrobial resistance.

Abstract: The invention enables efficient, rapid, and sensitive enumeration of living cells by detecting microscopic colonies derived from in situ cell division using large area imaging. Microbial enumeration tests based on the invention address an important problem in clinical and industrial microbiology—the long time needed for detection in traditional tests—while retaining key advantages of the traditional methods based on microbial culture. Embodiments of the invention include non-destructive aseptic methods for detecting cellular microcolonies without labeling reagents. These methods allow for the generation of pure cultures which can be used for microbial identification and determination of antimicrobial resistance.

Abstract: The invention enables efficient, rapid, and sensitive enumeration of living cells by detecting microscopic colonies derived from in situ cell division using large area imaging. Microbial enumeration tests based on the invention address an important problem in clinical and industrial microbiology—the long time needed for detection in traditional tests—while retaining key advantages of the traditional methods based on microbial culture. Embodiments of the invention include non-destructive aseptic methods for detecting cellular microcolonies without labeling reagents. These methods allow for the generation of pure cultures which can be used for microbial identification and determination of antimicrobial resistance.

Abstract: The invention features devices for capturing and culturing cells (e.g., microorganisms, cells containing microorganisms, or cells from eukaryotic cell cultures) and methods of using these devices. One device is a cassette containing growth media that may be employed in an automated rapid enumeration system. The cassette has, for example, been enhanced with features for controlling surface flatness, optical imaging, controlled dehydration of semi solid nutrient media, controlled air and particle exchange, and automated handling. Another device of the invention is a filtration funnel that may used to concentrate cells in a sample onto a membrane.