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 wireless, sterilizable scale comprising an upper module, on which an animal sits or explores, and a lower module that measures the weight of the animal. The lower module comprises a flexible membrane, through which the weight of the upper module and the animal is mechanically coupled. The flexible membrane is affixed at its perimeter to the perimeter of the lower module. The lower module is sealed by the membrane and comprises a load cell, batteries and electronics. The upper module removes easily from the lower module leaving the lower module intact and sealed for chemical sterilization. Electronics in the upper module connects to electronics in the lower module via an electrical connector that also penetrates the flexible membrane. IR communications from the upper modules transmits a series of weight values at two different data rates. The scale may be in a sterile cage free of electrical penetrations.

Abstract: A method of treating a patient for a disease, such as arthritis, is described. Steps include treating an animal for the disease with a first treatment, 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, and then computing an average of those values. This value is an efficacy and it is compared to a baseline efficacy. If the treatment is efficacious, the patient is so treated. A method of applying for a drug for approval is also described, using substantially the same steps.

Abstract: A method of measuring efficacy of test treatment of an autoimmune disease 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, a standard of care or a reference treatment for the first disease to determine efficacy of the test treatment. One embodiment quantifies an activity-drop by fitting straight-line curves through the data in the three nightly regions. Other embodiment uses a Fourier transform on a circle, LASSO, RANSAC or regression analyses for curve fitting. Another embodiment compares areas under data curves in the regions. Animals may be housed in cages with other animals.

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 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 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 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 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: 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 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: Methods of measuring gut transit time in animals are presented. Steps include fasting an animal, then feeding it a food containing a fluorescent dye, and then monitoring bedding for fluorescent droppings by using an ultraviolet (UV) fluorescent excitation light that is in the visible range of the animal, and thus is perceived by the animal as daylight, while turning off human-visible white light so that a camera may record UV emissions without faint emission light being burned out by human-visible light. Such methods are fully automatic with continual monitoring in the home-cage of the animal. Animals may be multi-housed with automated animal-ID. A single camera may be used to observe fluorescent emission light, animal activity under white light, and animal activity under infrared (IR) light. The method may be repeated to create a measurement sequence to determine matching to a disease model.

Abstract: A sterile scale is described suitable for automated use in animal cages. A case is covered by a flexible membrane that provides both sealing against pathogens and mechanical compliance for transfer of weight on an above weighing platform through a single sealed penetration in the membrane to a load cell in the case. The membrane comprises a perimeter that is attached and sealed to the case with a membrane frame, a penetration area, penetrated by a rigid weight-bearing element, and an isolating compliance area. A skirt on the weighing platform surrounds the case, protecting detritus from entering from below onto the membrane, while providing open-air movement. The weighing platform and case are easily separated permitting fluid-based sterilization of both. The weight-bearing element may contain an electrical connection from the case to the platform, through the membrane.

Abstract: A communicating sterile scale is described suitable for automated use in animal cages. An upper module provides a weighing platform, electronics, upward facing wireless communication elements, a protecting skirt, and interface to a combined weight-bearing and electrical penetration element. A lower module provides a case, internal electronics, load cell, power source, sterile-sealed flexible complaint membrane and a combined weight bearing and electrical penetration element through the membrane. The upper and lower modules are easily separable for sterilization by immersion in a sterilizing fluid. The power source in the case may be charged through same electrical penetrating element. The membrane comprises a perimeter that is attached and sealed to the case, a penetration area penetrated by the rigid weight-bearing element, and an isolating compliance area. The skirt on upper module protects detritus from entering from below onto the membrane, while providing open-air movement.

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: 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.

Abstract: The invention describes an automated method, device and system for both husbandry and study purposes of animals by providing a heat reward for specific behavior. Embodiments include maintaining the cage temperature at a normal, comfortable temperature for the animals, such as mice, using radiant heat rather than conducted heat to provide the reward, using home cages for the animals, detecting the behavior fully automated, operating in animal darkness, and using cages that are free of electrical penetrations. Some embodiments have one animal in a cage. Some embodiments have or support multiple animals in a cage and include methods to detect automatically identify animals, locate animals in the cage and associate a behavior and reward for a specific animal. Some embodiments place all sensors and radiant heat sources outside the cage, or use infrared sources for both heating and for IR camera lighting.