Abstract: A method of measuring efficacy of treatment of multiple sclerosis (MS) in an animal in a vivarium is described. Animal activity data is collected at multiple times during the night. Sequential time regions of the night are identified as high-activity, activity-drop, or low-activity regions. Embodiments are described to quantify a drop, during the night, of an animal's activity level. These quantified activity-drop scalars for consecutive nights are accumulated in an animal health dataset. This dataset is compared to healthy animals or a standard of care to determine efficacy. One embodiment quantifies an activity-drop by fitting straight-line curves through the data in the three nightly regions. Another embodiment uses a Fourier transform on a circle and a linear combination. Another embodiment compares areas under data curves in the regions. Animals may be housed in cages with other animals.

Abstract: A method for determining at least one physiological characteristic of at least one experimental animal in a cage is disclosed. The method may include capturing at least one infrared image of the at least one experimental animal in a band of infrared radiation that is within the range of from about 3 ?m to about 14 ?m in wavelength and capturing at least one visible image of the at least one experimental animal. The method may further include correlating the at least one image and the at least one visible light image and determining the at least one physiological characteristic of the at least one experimental animal based at least in part on the correlation. An apparatus to determine at least one physiological characteristic of at least one experimental animal is also disclosed.

Abstract: A cage for monitoring an experimental animal is disclosed. The cage may include one or more walls that enclose a living space for at least one experimental animal. At least one of the one or more walls may include a first material that is a plastic material. The cage may further include a window that is transparent to a band of infrared radiation that is within the range of from about 3 ?m to about 14 ?m in wavelength. The transparent window may have an inner side exposed to the living space that includes a second material that is substantially non-toxic to the at least one experimental animal.

Abstract: An animal exercise device is described in the form a rotating wheel, generally cylindrical in form, open on one face for an animal to enter and exit, and solidly closed on the other face, which also provides a bearing for rotation. The wall and closed face are solid to avoid injury to an animal. The wheel's axis of rotation is at an angle from horizontal. The inside surface of the wall comprises spaced ridges for gripping by the animal's toes or feet. A contrasting marking on the outside surface of the wall aids vision-based rotation measurement. Embodiments are supported solely through the bearing and have no rotation drive other than use by an animal. Methods of use include automated measurement, using equipment external to the cage, of animal health and use in a multihoused cage where unique animal ID is associated with wheel use.

Abstract: The field of this invention is recording motion of an animal, uniquely identifying the animal, and recording an activity of that animal. Motions of animals on a path when the animal is or can be uniquely identified are tracklets. Tracklets begin and end at ambiguation events, where these are defined as locations and times of an animal where it cannot be uniquely identified. A first animal may be uniquely identified by first identifying all other animals in the first animal's environment. Animal identification may be after the end of a tracklet. Embodiments use optical flow analysis from video of an animal's environment. Embodiments record an animal's activity on tracklets and then use that activity to measure animal health or use that activity as data for a study using animals.

Abstract: A device, system and method of equipment sets, “furniture,” to provide animal husbandry functions are described. Embodiments include: a frame in the form of a ring adapted to sit in a single possible orientation within an animal cage, wherein the frame comprises hollow, open-top vertical columns, adapted to receive pieces of furniture comprising mating pins; a running wheel mounted on a axle integral to the monolithic frame; a horizontal climbing ladder; and a food tray. Embodiments include feet extending from the frame for fixed positioning within a cage; a reserved area to hold a weight scale; curved corners for cage fit; monolithic construction of all individual elements; a canted wheel axis; a sloped inner edge of a food tray to permit unobstructed views of animals in a cage. Methods include assembly; use in an animal cage; and use to observe and measure animal activity using husbandry-only procedures for the animals; and for animal studies using non-invasive procedures.

Abstract: Aggregates of sets of identification tags are described, such as may be used on animals, such as mice or rats, affixed to ears or attached otherwise to an animal. A set may comprise from two to five patterns. An aggregate may comprise one to five sets. Patterns comprise a perimeter with an interior contrasting field, optional contrasting shapes within the field, and an optional contrasting shape core within a shape. Simple shapes may be squares, circles, or triangles. Shapes are selected for maximum machine readability. A pattern may have from zero to three shapes in its field. Patterns within sets are selected for maximum differentiation between the patterns in the set. Aggregates are selected based on the number of different sets required. Identification tags may be used to uniquely identify animals in a cage. Shown are specific patterns for embodiments of devices, systems and methods.

Abstract: A method of early detection of multiple sclerosis (MS) in an animal in a vivarium is described. Animal activity data is collected at multiple times during the night. Sequential time regions of the night are identified as high-activity, activity-drop, or low-activity regions. Embodiments are described to quantify a drop, during the night, of an animal's activity level. These quantified activity-drop scalars for consecutive nights are accumulated in an animal health dataset. Then, a health detection function is applied to this dataset that, in response to the level of activity change and the speed of activity change, predicts or detects MS in the animal. One embodiment quantifies an activity-drop by fitting straight-line curves through the data in the three nightly regions. Another embodiment uses a Fourier transform on a circle and a linear combination. Another embodiment compares areas under data curves in the regions. Animals may be housed in cages with other animals.

Abstract: A modular vivarium is assembled from pre-manufactured, transportable, sterile modules of distinct types, called pods. A hallway pod forms a spine, with cage-rack pods, ingress/egress pods and optional HVACPIT pods providing HVAC, power and IT services connected as spur pods to the hallway. Supplies and waste are also within modular pods. Temporary or single-use seals cover doorways during transit. Modules are joined or removed while maintaining sterility on both sides of the flush-to-wall doorway junction. A spur pod is sterilely connected to a hallway pod by aligning respective doors proximal, placing a seal between the pods around the doorways, sterilizing air between the pods, then removing the temporary seals from each doorway. Pods may be constructed from easily transportable ISO intermodal containers.

Abstract: A respiration rate detector is provided for determining a rate of respiration of an experimental animal. The respiration rate detector includes one or more optical detectors to observe an experimental animal and generate a video signal relating to the experimental animal. A controller is provided to process the video signal to determine an optical flow of the video signal and generate an optical-flow signal, and analyze the optical-flow signal to determine the respiration rate of the experimental animal based on a detected repetitive movement of the experimental animal. The respiration rate is thereby detected without requiring physical contact with the experimental animal.

Abstract: A test pad comprising multiple test patches and urine detection patches in an array is described. The test pad is suitable for automated urine analysis of multiple animals in a cage. Urine detection patches may be arranged in a BAYER pattern or as rings. Multiple layers, including a substrate, a wicking layer, a test patch layer, and optional protection layer serve to manage puddles of urine. Various isolation elements are described that keep urine puddles from spreading. Color reference spots on the pad are used for dynamic color determination of test patches. Urine detection patches start a read clock and identify which test patches are valid. Elements to hold and align the test pad are described. Methods of detection and reading are described.

Abstract: A method of reading arbitrary symbols is described. Symbols may degrade over time. Shapes of symbols as they degrade are used to update an initial symbol library, which is created based on actual markings, rather than idealized symbols. Marks associate with shapes, which associate to symbols, which in aggregate associate with an object ID. A read mark is compared to all the shapes in the library to determine a most likely shape. A selection set is used to limit shape selection, based on the comparison, to shapes of valid symbols. Comparison methods use probability distributions. Confidence values are used to validate output, generate warnings, and to control updating of the library. Weighted averaging based on confidence values or age of reads may be used at the level of shapes, comparison distributions, or selections.

Abstract: A method of early detection of multiple sclerosis (MS) in an animal in a vivarium is described. Animal activity data is collected at multiple times during the night. Sequential time regions of the night are identified as high-activity, activity-drop, or low-activity regions. Embodiments are described to quantify a drop, during the night, of an animal's activity level. These quantified activity-drop scalars for consecutive nights are accumulated in an animal health dataset. Then, a health detection function is applied to this dataset that, in response to the level of activity change and the speed of activity change, predicts or detects MS in the animal. One embodiment quantifies an activity-drop by fitting straight-line curves through the data in the three nightly regions. Another embodiment uses a Fourier transform on a circle and a linear combination. Another embodiment compares areas under data curves in the regions. Animals may be housed in cages with other animals.

Abstract: The field of this invention is classifying animal behaviors. In particular the fields of this invention include using animals in vivariums, such as rodents, particularly mice. Animal behaviors are classified according to behaviors consistent with healthy or unhealthy organs or locations within organs, such as the brain. Injected neoplastic cells may be used to create an unhealthy organ or location within an organ. Classifications also include responses to different therapies. The behavior of the animals is observed using fully automatic, continuous monitoring using per-cage ultrasonic and video sensors, where behavior recording is free of human, manual actions. Observed behavior is consistent with healthy or unhealthy behaviors specific to the injection site. Both positive and negative baseline behaviors are collected, typically using the same system or method.

Abstract: The field of this invention is classifying animal behaviors. In particular the fields of this invention include using animals in vivariums, such as rodents, particularly mice. In a vivarium cage, mice generate ultrasonic vocalizations and video behaviors. Their phenotype may also change. Starting with known cognitions or emotions, then comparing the vocalizations, changes to phenotype and video behaviors identification, classification and correlations of cognition or emotion may be generated. These new identifications, classifications and correlations are then used to update the starting set of cognition and emotion of the study animals, in a continuous feedback.

Abstract: The field of this invention is classifying animal behaviors. In particular the fields of this invention include using animals in vivariums, such as rodents, particularly mice. Ultrasonic vocalizations of mice in a vivarium are compared to a predetermined set of positive phenotypes and to a predetermined set of negative phenotypes. The output of those comparisons are then compared to determine a metric of distance to classify vocalizations as closer to or more distant from elements of the positive or negative sets.

Abstract: The field of this invention is classifying animal behaviors. In particular the fields of this invention include using animals in vivariums, such as rodents, particularly mice. In a vivarium cage, animals create ultrasonic vocalizations. In addition, their phenotype changes over time. The vocalizations, a current phenotype, and the cage environments are inputs to a multi-dimensional classifier using clustering algorithms to find multi-dimensional close relationships. Such close relationships may be identified as particular behavior.

Abstract: The field of this invention is classifying animal behaviors. In particular the fields of this invention include using animals in vivariums, such as rodents, particularly mice. Ultrasonic vocalizations are compared to times-shifted video behaviors of the same mice to identify vocalizations that occur prior to, during, and after particular video behaviors. The comparisons generate correlations weights that may then be used to apply known classifications of the video behaviors to the vocalizations.

Abstract: A method of measuring animal health, such as rodent health, such as a degree of arthritis, is described. Steps include capturing video frames, then using optical flow to compute vector fields for each frame, then taking a maximum vector value over a first time period, then selecting a set of maximum vector values over a second time period, then clipping those values to a maximum, then computing an average of those values. This is an animal health metric. Metrics may be organized into a plot over time and may then be compared against known plots to compute an overall animal health and measure efficacy of treatments or other animal characteristics or behavior, including predictive.

Abstract: A method of reading degraded symbols is described. A symbol has an initial shape, which is marked on an object. Marks, shapes, symbols, and object ID are managed separately. A symbol library with symbols and associated shapes is initially created. Shapes in the library are updated from shapes of marks as the marks degrade over time. A read mark is compared to all the shapes in the library to determine a most likely shape. A selection set is used to limit symbol selection, based on the comparison, to valid symbols. The symbol library and selection set may be customized to each usage of the method. Comparison methods use probability distributions. Confidence values are used to validate output, generate warnings, and to control updating of the library. Weighted averaging may be used at the level of shapes, comparison distributions, or selections. One application is reading tattooed marks on rodent tails in a vivarium.