Abstract: A modular vivarium is constructed entirely from transportable, sterile modules of distinct types, called pods. A hallway pod forms a spine, with cage-rack pods, ingress/egress pods and optional VHACPIT 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. Supply and return air for all pods is through hallway based ducting. Pods may be constructed from ISO intermodal containers. Embodiments have no permanent buildings. Pods may be moved, leveled and aligned for joining via special supports. Cage-rack pods are configured with two cage racks and a single isle permitting robotic cage placement and retrieval. Embodiments provide vibration, noise and earthquake isolation.

Abstract: An animal cage is described suitable for automated use in a vivarium. The cage comprises a study animal; bedding; pathogens; a wireless, a sterilizable scale comprising a sterile case comprising a flexible, penetrated membrane; and a penetrating fastener penetrating the membrane. The comprises four internal volume areas with respect to pathogen content: (1) volume between the membrane and a weighing platform, free of bedding; (2) a sterile volume inside the scale case below the membrane; (3) a vertical channel fluidly connecting the inside of the cage with the first volume; and (4) the inside of the cage outside of the above three volumes. These four volumes are sterilely isolated from air outside the cage. Electronics in the scale communicate wirelessly, through the cage, to cage-associated electronics outside the cage, using narrow beam communications free of device-ID specific protocol. The scale may be disassembled, sterilized in a fluid, re-assembled, and re-used in a different cage.

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: 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. When two mice socialize, a first mouse vocalizes a call and the second mouse vocalizes a response. Ultrasonic calls and responses are compared to video behaviors of the same mice, and then a table is constructed where each line comprises a particular call and response, a corresponding video behavior, and a correlation weight.

Abstract: A method for electronically determining a metabolic characteristic of an experimental animal in a living space is disclosed. The method includes confirming that a temperature in a living space is within a predefined range that consists of temperatures near or within a metabolic thermoneutral zone of the experimental animal, capturing at least one infrared image of 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, identifying at least one data set of the at least one infrared image that corresponds to a tail of the experimental animal, processing the at least one data set of the at least one infrared image to evaluate a temperature of the tail of the experimental animal, and determining the metabolic characteristic based at least in part on the evaluated tail temperature.

Abstract: A doorway interconnection and method of creating an airtight seal between two doorways includes a first temporary membrane creating an airtight seal on a first doorway and a second temporary membrane creating an airtight seal on a second doorway and a gasket between the two doorways, and vents and valves to place and remove a sterilizing fluid in the inter-doorway volume. Such a system may be used to attach a sterile modular building unit to a sterile facility without losing the sterility of either the facility or the module building unit. Access to the membranes may be from one direction only. The gasket may provide motion and sound isolation between. Additional elements limit relative motions between the first and second doorways.

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 monitoring device and method comprising an animal cage and associated electronics slab is described. The device is suitable for use in a modular vivarium implemented in one or two racks adjacent to walls in a holding pod. There is a one-to-one relationship between fixed slabs and removable cages. A single camera provides range of functions: its field of view includes the entire area of the cage accessible to an animal; it may observe water level in a water bottle; it may observe food level in a food tray; it may view activity on an exercise device; it may read the rear of cage card. The shape of the food tray is specialized to meet these requirements. An inner-cage frame holds elements in fixed locations within the cage. The cage is free of electronic penetrations. Supply and return air for the cage passes through the slab.

Abstract: Methods of automatically measuring a reaction time of an animal, in a cage, to a stimulus, are described. First, an animal is detected, then a second apparatus waits for the animal to be fully on the apparatus. A first apparatus outside the cage then provides a stimulus. A second, sterilizable, wireless apparatus inside the cage measures a response of the animal such a jerk, using an accelerometer. The first and second apparatuses time-synchronize. The second device transmits wirelessly the response time data, after optional preprocessing, to the first apparatus. For multi-housed animals, an ID of the animal is determined. The second apparatus may comprise an animal weight scale.

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 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.

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 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 of collecting data for treatment of disease in vivarium animals 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 an activity-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. 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. Additional functions may be applied to the activity changes in the dataset to detect disease, measure severity, measure efficacy, or predict outcomes.

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 method of predicting severity 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, an MS severity index function is applied to this dataset that, in response to the level of activity change and the speed of activity change, predicts or measures severity of 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: 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.