Abstract: Methods of measuring attributes of animal urine, using a test pad comprising multiple test patches and urine detection patches in a BAYER pattern is described. The pad comprises different test patches, each surrounded by urine detection patches. When a camera, electronics and software automatically detect fresh urine from a color change of a detection patch, nearby test patches are read with a color camera, after a specific time delay, and compared to color reference spots. Multiple layers and isolation zones in the test pad allow urine to enter the test and detection patches, while keeping urine puddles from spreading. Once used, detection and test patches are not used again. An array of many detection and test patches allows the test pad to be used for multiple urine samples in one vivarium cage before replacing. Embodiments use a mix of IR and white light, and IR cameras and color cameras.

Abstract: A method of determining a cognitive state of an experimental animal in a cage is provided. The cage includes one or more walls that enclose a living space for containing the experimental animal, and a heating structure. The method includes installing a card with at least a first type of sequestered olfactory compound, directing the heating structure to selectively heat the card to release the first type of sequestered first type of olfactory compound to subject the experimental animal to a novel olfactory experience, creating a first assessment of a behavior of the laboratory animal, subjecting the experimental animal to experimental procedures and/or waiting a selected amount of time, directing the heating structure to selectively heat the card to release more of the first type of sequestered olfactory compound, creating a second assessment of a behavior of the experimental animal, and evaluating the first and second assessments to determine the cognitive state of the experimental animal.

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: 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: A machine suitable for marking codes on rodent tails is disclosed, for marking both machine-readable and human-readable codes and such codes combined. An embodiment comprises two axes of motion: one aligned with the rodent tail and one perpendicular. Only one axis need move at one time for disclosed codes. One axis is linear motion of a marking head on a gantry. The second axis provides a rolling motion of the rodent tail. Codes include symbol sets consisting of orthogonal straight line segments, including both a reduced alphanumeric symbols set and a vine code with a marked spine. Delete markings and replacement locations are defined for marking error correction. Embodiments include mapping tables from animal codes as marked to animal IDs for use in managing animals in vivaria. The mapping tables also provide error detection.

Abstract: A test pad comprising multiple urine attribute patches and urine detection patches in a BAYER pattern is described. The test pad is suitable for automated urine analysis of multiple animals in a cage. Generalized detection patches may be arranged adjacent to and surrounding each individual test patch for a specific urine attribute. First, fresh urine is detected in a detection patch with a camera; a timer is started; then adjacent urine attribute patches are read. Once a test patch has been used once it is disregarded for future analysis.

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: 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 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: An animal identification code is described comprising two numbers, one of which is encoded into a human-readable marking and the other of which is encoded into a machine-readable marking, where the two numbers and the two encodings are different. The combination of the two numbers, plus additional information not marked on a first animal, such as time of read, is looked up a first table to determine conditional validity and from there to a second table to determine a valid and unique animal ID associated with the animal, a primary key. The animal may be a rodent in a vivarium and the markings may be tattooed on the animal tail. The second marking may be a vine code with a spine where the spine is aligned with the animal tail. The first number may be unique within a first animal population such as an animal study. The combination of the first and second marking may be reused on a second animal wherein the lifetimes of the first and second animal do not overlap.

Abstract: A method of generating animal identification codes is described. A first and second number are selected, then each number is compared respectively against previously used first and previously used second numbers in a pool. Such comparing uses a computed distance based on how the numbers will be encoded and marked on an animal, such as a Hamming distance of printed symbologies. If the distance computed for either the first or second number is below a distance threshold, that number is discarded and another number is selected. When both numbers pass the distance test, they are added as a pair into the pool. Pairs from the pool may be encoded and marked on an animal. The encoding of the first number may generate a human-readable mark while a different encoding of the second number generates a machine-readable mark.

Abstract: An animal identification code is described comprising two numbers, one of which is encoded into a human-readable marking and the other of which is encoded into a machine-readable marking, where the two numbers and the two encodings are different. The combination of the two numbers, plus additional information not marked on a first animal, such as time of read, is looked up a first table to determine conditional validity and from there to a second table to determine a valid and unique animal ID associated with the animal, a primary key. The animal may be a rodent in a vivarium and the markings may be tattooed on the animal tail. The second marking may be a vine code with a spine where the spine is aligned with the animal tail. The first number may be unique within a first animal population such as an animal study. The combination of the first and second marking may be reused on a second animal wherein the lifetimes of the first and second animal do not overlap.

Abstract: An animal identification code is described comprising two numbers, one of which is encoded into a human-readable marking and the other of which is encoded into a machine-readable marking, where the two numbers and the two encodings are different. The combination of the two numbers, plus additional information not marked on a first animal, such as time of read, is looked up a first table to determine conditional validity and from there to a second table to determine a valid and unique animal ID associated with the animal, a primary key. The animal may be a rodent in a vivarium and the markings may be tattooed on the animal tail. The second marking may be a vine code with a spine where the spine is aligned with the animal tail. The first number may be unique within a first animal population such as an animal study. The combination of the first and second marking may be reused on a second animal wherein the lifetimes of the first and second animal do not overlap.

Abstract: An animal identification code is described comprising two numbers, one of which is encoded into a human-readable marking and the other of which is encoded into a machine-readable marking, where the two numbers and the two encodings are different. The combination of the two numbers, plus additional information not marked on a first animal, such as time of read, is looked up a first table to determine conditional validity and from there to a second table to determine a valid and unique animal ID associated with the animal, a primary key. The animal may be a rodent in a vivarium and the markings may be tattooed on the animal tail. The second marking may be a vine code with a spine where the spine is aligned with the animal tail. The first number may be unique within a first animal population such as an animal study. The combination of the first and second marking may be reused on a second animal wherein the lifetimes of the first and second animal do not overlap.

Abstract: A method of generating animal identification codes is described. A first and second number are selected, then each number is compared respectively against previously used first and previously used second numbers in a pool. Such comparing uses a computed distance based on how the numbers will be encoded and marked on an animal, such as a Hamming distance of printed symbologies. If the distance computed for either the first or second number is below a distance threshold, that number is discarded and another number is selected. When both numbers pass the distance test, they are added as a pair into the pool. Pairs from the pool may be encoded and marked on an animal. The encoding of the first number may generate a human-readable mark while a different encoding of the second number generates a machine-readable mark.

Abstract: A method of reading animal identification marks is described. Starting with a series of image frames of an animal, the location and angle of the animal is determined, then the curvature of the animal tail. Using modified frames with a straightened tail, character areas are identified. For a given output character set of a number encoding method, the probability is computed for each character in the set, of that character in each character area, for each frame. The probabilities for the character set for each character area are summed over the frames. Then, the most probable character is chosen for each character area. The chosen characters are combined into a number and verified as being a currently valid animal ID. If the number is not valid, a next most probable character is chosen. This method may be applied separately for a human-readable marking and a machine-readable marking, both on one animal.

Abstract: Symbologies suitable for use marking codes on rodent tails are disclosed, for both machine-readable and human-readable codes, and those codes combined. Codes comprising both a human-readable and a machine-readable portion may associate with an animal ID within one study, and a study ID within a vivarium, respectively. A human-readable code uses a subset of an alphanumeric symbol set. A machine-readable code uses a vine-code with a visible spine aligned with the rodent's tail. Both symbologies support a system for deleting symbols and correcting codes marked in error. Both symbologies use symbol sets comprising only horizontal and vertical line segments. Both symbologies include a sparse mapping table for mapping marking codes to animal and study ID, and for error detection and for code re-use.