text:
Calculations are performed on a series of frames to derive a set of quantitative descriptors of the animal's movement. EthoVision (from Noldus Information Technology) is a specific example of such a system, and its functionality that is particularly relevant to transgenic mice studies is described. Key practical aspects of using the EthoVision system are also outlined, including tips about lighting, marking animals, the arena size, and sample rate. Four case studies are presented, illustrating various aspects of the system: (1) The effects of disabling the Munc 18-1 gene were clearly shown using the straightforward measure of how long the mice took to enter a zone in an open field. (2) Differences in exploratory behavior between short and long attack latency mice strains were quantified by measuring the time spent in inner and outer zones of an open field. (3) Mice with hypomorphic CREB alleles were shown to perform less well in a water maze, but this was only clear when a range of different variables were calculated from their tracks. (4) Mice with the trkB receptor knocked out in the forebrain also performed poorly in a water maze, and it was immediately apparent from examining plots of the tracks that this was due to thigmotaxis. Some of the latest technological developments and possible future directions for video tracking systems are briefly discussed.},
	number = {5},
	urldate = {2019-07-28},
	journal = {Physiology \& Behavior},
	author = {Spink, A. J and Tegelenbosch, R. A. J and Buma, M. O. S and Noldus, L. P. J. J},
	month = aug,
	year = {2001},
	keywords = {Automated observation, Rodent, Video tracking, Water maze},
	pages = {731--744}
}

@article{dunne_development_2007,
	title = {Development of a home cage locomotor tracking system capable of detecting the stimulant and sedative properties of drugs in rats},
	volume = {31},
	issn = {0278-5846},
	url = {http://www.sciencedirect.com/science/article/pii/S0278584607002163},
	doi = {10.1016/j.pnpbp.2007.06.023},
	abstract = {The advent of automated locomotor activity methodologies has been extremely useful in removing the subjectivity and bias out of measuring this parameter in rodents. However, many of these behavioural studies are still conducted in novel environments, rather than in ones that the animals are familiar with, such as their home cage. The purpose of the present series of experiments was to develop an automated home cage tracking (HCT) profile using EthoVision® software and assessing the acute effects of stimulant (amphetamine and methamphetamine, 0–5 mg/kg, sc) and sedative (diazepam, 0–20 mg/kg, sc and chlordiazepoxide, 0–50 mg/kg sc) drugs in this apparatus. Young adult male Sprague–Dawley rats were used, and the home cage locomotor activity was recorded for 11–60 min following administration (n=4 per group). For amphetamine and methamphetamine, a dose-dependent increase in home cage activity was evident for both drugs, with a plateau, followed by reduction at higher doses. Methamphetamine was more potent, whereas amphetamine produced greater maximal responses. Both diazepam and chlordiazepoxide dose-dependently reduced locomotor activity, with diazepam exhibiting a greater potency and having stronger sedative effects than chlordiazepoxide. Three doses of each drug were selected at the 31–40 min time period following administration, and compared to open field responses. Diazepam, chlordiazepoxide and amphetamine did not produce significant changes in the open field, whilst methamphetamine produced a significant increase in the 2.5 mg/kg group. In conclusion, these studies have successfully developed a sensitive HCT methodology that has been validated using drugs with stimulant and sedative properties in the same test conditions, with relatively small numbers of animals required to produce statistically significant results. It has proven superior to the open field investigations in allowing dose-response effects to be observed over a relatively short observation period (i.e. 10 min) for both stimulants and sedatives. In addition, the HCT system can determine differences in potency and efficacy between drugs of a similar chemical class.},
	number = {7},
	urldate = {2019-07-28},
	journal = {Progress in Neuro-Psychopharmacology and Biological Psychiatry},
	author = {Dunne, Fergal and O'Halloran, Ambrose and Kelly, John P.},
	month = oct,
	year = {2007},
	keywords = {Home cage, Locomotor activity, Rats, Sedatives, Stimulants},
	pages = {1456--1463}
}

@article{young_combined_2000,
	title = {A combined system for measuring animal motion activities},
	volume = {95},
	issn = {0165-0270},
	url = {http://www.sciencedirect.com/science/article/pii/S0165027099001569},
	doi = {10.1016/S0165-0270(99)00156-9},
	abstract = {In this study, we have developed a combined animal motion activity measurement system that combines an infrared light matrix subsystem with an ultrasonic phase shift subsystem for animal activity measurement. Accordingly, in conjunction with an IBM PC/AT compatible personal computer, the combined system has the advantages of both infrared and ultrasonic subsystems. That is, it can at once measure and directly analyze detailed changes in animal activity ranging from locomotion to tremor. The main advantages of this combined system are that it features real time data acquisition with the option of animated real time or recorded display/playback of the animal’s motion. Additionally, under the multi-task operating condition of IBM PC, it can acquire and process behavior using both IR and ultrasound systems simultaneously. Traditional systems have had to make separate runs for gross and fine movement recording. This combined system can be profitably employed for normative behavioral activity studies and for neurological and pharmacological research.},
	number = {1},
	urldate = {2019-07-28},
	journal = {Journal of Neuroscience Methods},
	author = {Young, M. S. and Young, C. W. and Li, Y. C.},
	month = jan,
	year = {2000},
	keywords = {Animal activity, Infrared Light, Measurement, Real time, Single-chip microcomputer, Ultrasound},
	pages = {55--63}
}

@article{aragao_automatic_2011,
	title = {Automatic system for analysis of locomotor activity in rodents—{A} reproducibility study},
	volume = {195},
	issn = {0165-0270},
	url = {http://www.sciencedirect.com/science/article/pii/S0165027010007041},
	doi = {10.1016/j.jneumeth.2010.12.016},
	abstract = {Automatic analysis of locomotion in studies of behavior and development is of great importance because it eliminates the subjective influence of evaluators on the study. This study aimed to develop and test the reproducibility of a system for automated analysis of locomotor activity in rats. For this study, 15 male Wistar were evaluated at P8, P14, P17, P21, P30 and P60. A monitoring system was developed that consisted of an open field of 1m in diameter with a black surface, an infrared digital camera and a video capture card. The animals were filmed for 2min as they moved freely in the field. The images were sent to a computer connected to the camera. Afterwards, the videos were analyzed using software developed using MATLAB® (mathematical software). The software was able to recognize the pixels constituting the image and extract the following parameters: distance traveled, average speed, average potency, time immobile, number of stops, time spent in different areas of the field and time immobile/number of stops. All data were exported for further analysis. The system was able to effectively extract the desired parameters. Thus, it was possible to observe developmental changes in the patterns of movement of the animals. We also discuss similarities and differences between this system and previously described systems.},
	number = {2},
	urldate = {2019-07-28},
	journal = {Journal of Neuroscience Methods},
	author = {Aragão, Raquel da Silva and Rodrigues, Marco Aurélio Benedetti and de Barros, Karla Mônica Ferraz Teixeira and Silva, Sebastião Rogério Freitas and Toscano, Ana Elisa and de Souza, Ricardo Emmanuel and Manhães-de-Castro, Raul},
	month = feb,
	year = {2011},
	keywords = {Automated analysis, Behavioral analysis, Biomechanical analysis, Locomotor activity, Open field},
	pages = {216--221}
}

@article{benjamini_ten_2010,
	title = {Ten ways to improve the quality of descriptions of whole-animal movement},
	volume = {34},
	issn = {0149-7634},
	url = {http://www.sciencedirect.com/science/article/pii/S0149763410000886},
	doi = {10.1016/j.neubiorev.2010.04.004},
	abstract = {The demand for replicability of behavioral results across laboratories is viewed as a burden in behavior genetics. We demonstrate how it can become an asset offering a quantitative criterion that guides the design of better ways to describe behavior. Passing the high benchmark dictated by the replicability demand requires less stressful and less restraining experimental setups, less noisy data, individually customized cutoff points between the building blocks of movement, and less variable yet discriminative dynamic representations that would capture more faithfully the nature of the behavior, unmasking similarities and differences and revealing novel animal-centered measures. Here we review ten tools that enhance replicability without compromising discrimination. While we demonstrate the usefulness of these tools in the context of inbred mouse exploratory behavior they can readily be used in any study involving a high-resolution analysis of spatial behavior. Viewing replicability as a design concept and using the ten methodological improvements may prove useful in many fields not necessarily related to spatial behavior.},
	number = {8},
	urldate = {2019-07-28},
	journal = {Neuroscience \& Biobehavioral Reviews},
	author = {Benjamini, Yoav and Lipkind, Dina and Horev, Guy and Fonio, Ehud and Kafkafi, Neri and Golani, Ilan},
	month = jul,
	year = {2010},
	keywords = {Compression of kinematic data, Description of behavior, Discriminability between strains and preparations, Exploratory behavior, Genotype-laboratory interaction, Mixed-Model Anova, Open field behavior, Phenotyping mouse behavior, Replicability of results, Segmentation of behavior, Smoothing kinematic data},
	pages = {1351--1365}
}

@article{Arpteg2018SoftwareEC,
  title={Software Engineering Challenges of Deep Learning},
  author={A. Arpteg and B. Brinne and Luka Crnkovic-Friis and J. Bosch},
  journal={2018 44th Euromicro Conference on Software Engineering and Advanced Applications (SEAA)},
  year={2018},
  pages={50-59},
  doi={10.1109/seaa.2018.00018},
}

@InProceedings{ mckinney-proc-scipy-2010,
  author    = { {W}es {M}c{K}inney },
  title     = { {D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython },
  booktitle = { {P}roceedings of the 9th {P}ython in {S}cience {C}onference },
  pages     = { 56 - 61 },
  year      = { 2010 },
  editor    = { {S}t\'efan van der {W}alt and {J}arrod {M}illman },
  doi       = { 10.25080/Majora-92bf1922-00a }
}

@article{van_galen_effects_1990,
	title = {Effects of motor programming on the power spectral density function of finger and wrist movements},
	volume = {16},
	issn = {1939-1277(Electronic),0096-1523(Print)},
	doi = {10.1037/0096-1523.16.4.755},
	abstract = {Power spectral density analysis was applied to the frequency content of the acceleration signal of pen movements in line drawing using 10 right-handed college students. The relative power in frequency bands between 1 and 32 Hz was measured as a function of motoric and anatomic task demands. Results showed a decrease of power at the lower frequencies (1–4 Hz) of the spectrum and an increase in the middle (9–22 Hz) with increasing motor demands. These findings evidence the inhibition of visual control and the disinhibition of physiological tremor under conditions of increased programming demands. Adductive movements displayed less power than abductive movements in the lower end of the spectrum, with a simultaneous increase at the higher frequencies. The relevance of the method for the measurement of neuromotor noise as a possible origin of delays in motor behavior is discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved)},
	number = {4},
	journal = {Journal of Experimental Psychology: Human Perception and Performance},
	author = {Van Galen, Gerard P. and Van Doorn, Robert R. and Schomaker, Lambert R.},
	year = {1990},
	note = {Place: US
Publisher: American Psychological Association},
	keywords = {Fingers (Anatomy), Motion Perception, Task Complexity, Wrist},
	pages = {755--765},
}

@software{reback2020pandas,
    author       = {The pandas development team},
    title        = {pandas-dev/pandas: Pandas},
    month        = feb,
    year         = 2020,
    publisher    = {Zenodo},
    version      = {latest},
    doi          = {10.5281/zenodo.3509134},
    url          = {https://doi.org/10.5281/zenodo.3509134}
}

@article{noonan_scale-insensitive_2019,
	title = {Scale-insensitive estimation of speed and distance traveled from animal tracking data},
	volume = {7},
	issn = {2051-3933},
	url = {https://doi.org/10.1186/s40462-019-0177-1},
	doi = {10.1186/s40462-019-0177-1},
	abstract = {Speed and distance traveled provide quantifiable links between behavior and energetics, and are among the metrics most routinely estimated from animal tracking data. Researchers typically sum over the straight-line displacements (SLDs) between sampled locations to quantify distance traveled, while speed is estimated by dividing these displacements by time. Problematically, this approach is highly sensitive to the measurement scale, with biases subject to the sampling frequency, the tortuosity of the animal’s movement, and the amount of measurement error. Compounding the issue of scale-sensitivity, SLD estimates do not come equipped with confidence intervals to quantify their uncertainty.},
	number = {1},
	urldate = {2021-02-13},
	journal = {Movement Ecology},
	author = {Noonan, Michael J. and Fleming, Christen H. and Akre, Thomas S. and Drescher-Lehman, Jonathan and Gurarie, Eliezer and Harrison, Autumn-Lynn and Kays, Roland and Calabrese, Justin M.},
	month = nov,
	year = {2019},
	keywords = {Continuous-time, GPS, correlated velocity, ctmm, movement models, step length, telemetry, travel distance},
	pages = {35},
}

@misc{noauthor_f1000workspace_nodate-1,
	title = {F1000Workspace},
	url = {https://f1000.com/work/#/items/6352976},
	urldate = {2019-07-28}
}

@article{kilkenny_improving_2010,
	title = {Improving {Bioscience} {Research} {Reporting}: {The} {ARRIVE} {Guidelines} for {Reporting} {Animal} {Research}},
	volume = {8},
	issn = {1545-7885},
	shorttitle = {Improving {Bioscience} {Research} {Reporting}},
	url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000412},
	doi = {10.1371/journal.pbio.1000412},
	language = {en},
	number = {6},
	urldate = {2019-07-28},
	journal = {PLOS Biology},
	author = {Kilkenny, Carol and Browne, William J. and Cuthill, Innes C. and Emerson, Michael and Altman, Douglas G.},
	month = jun,
	year = {2010},
	keywords = {Laboratory animals, Peer review, Research design, Research laboratories, Research reporting guidelines, Routes of administration, Statistical data, Statistical methods},
	pages = {e1000412}
}

@article{fisher_update_2009,
	title = {Update of the {Stroke} {Therapy} {Academic} {Industry} {Roundtable} {Preclinical} {Recommendations}},
	volume = {40},
	issn = {0039-2499},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888275/},
	doi = {10.1161/STROKEAHA.108.541128},
	abstract = {The initial Stroke Therapy Academic Industry Roundtable (STAIR) recommendations published in 1999 were intended to improve the quality of preclinical studies of purported acute stroke therapies. Although recognized as reasonable, they have not been closely followed nor rigorously validated. Substantial advances have occurred regarding the appropriate quality and breadth of preclinical testing for candidate acute stroke therapies for better clinical translation. The updated STAIR preclinical recommendations reinforce the previous suggestions that reproducibly defining dose response and time windows with both histological and functional outcomes in multiple animal species with appropriate physiological monitoring is appropriate. The updated STAIR recommendations include: the fundamentals of good scientific inquiry should be followed by eliminating randomization and assessment bias, a priori defining inclusion/exclusion criteria, performing appropriate power and sample size calculations, and disclosing potential conflicts of interest. After initial evaluations in young, healthy male animals, further studies should be performed in females, aged animals, and animals with comorbid conditions such as hypertension, diabetes, and hypercholesterolemia. Another consideration is the use of clinically relevant biomarkers in animal studies. Although the recommendations cannot be validated until effective therapies based on them emerge from clinical trials, it is hoped that adherence to them might enhance the chances for success.},
	number = {6},
	urldate = {2019-07-28},
	journal = {Stroke; a journal of cerebral circulation},
	author = {Fisher, Marc and Feuerstein, Giora and Howells, David W. and Hurn, Patricia D. and Kent, Thomas A. and Savitz, Sean I. and Lo, Eng H.},
	month = jun,
	year = {2009},
	pmid = {19246690},
	pmcid = {PMC2888275},
	pages = {2244--2250}
}

@article{engel_modeling_2011,
	title = {Modeling stroke in mice - middle cerebral artery occlusion with the filament model},
	issn = {1940-087X},
	doi = {10.3791/2423},
	abstract = {Stroke is among the most frequent causes of death and adult disability, especially in highly developed countries. However, treatment options to date are very limited. To meet the need for novel therapeutic approaches, experimental stroke research frequently employs rodent models of focal cerebral ischaemia. Most researchers use permanent or transient occlusion of the middle cerebral artery (MCA) in mice or rats. Proximal occlusion of the middle cerebral artery (MCA) via the intraluminal suture technique (so called filament or suture model) is probably the most frequently used model in experimental stroke research. The intraluminal MCAO model offers the advantage of inducing reproducible transient or permanent ischaemia of the MCA territory in a relatively non-invasive manner. Intraluminal approaches interrupt the blood flow of the entire territory of this artery. Filament occlusion thus arrests flow proximal to the lenticulo-striate arteries, which supply the basal ganglia. Filament occlusion of the MCA results in reproducible lesions in the cortex and striatum and can be either permanent or transient. In contrast, models inducing distal (to the branching of the lenticulo-striate arteries) MCA occlusion typically spare the striatum and primarily involve the neocortex. In addition these models do require craniectomy. In the model demonstrated in this article, a silicon coated filament is introduced into the common carotid artery and advanced along the internal carotid artery into the Circle of Willis, where it blocks the origin of the middle cerebral artery. In patients, occlusions of the middle cerebral artery are among the most common causes of ischaemic stroke. Since varying ischemic intervals can be chosen freely in this model depending on the time point of reperfusion, ischaemic lesions with varying degrees of severity can be produced. Reperfusion by removal of the occluding filament at least partially models the restoration of blood flow after spontaneous or therapeutic (tPA) lysis of a thromboembolic clot in humans. In this video we will present the basic technique as well as the major pitfalls and confounders which may limit the predictive value of this model.},
	language = {eng},
	number = {47},
	journal = {Journal of Visualized Experiments: JoVE},
	author = {Engel, Odilo and Kolodziej, Sabine and Dirnagl, Ulrich and Prinz, Vincent},
	month = jan,
	year = {2011},
	pmid = {21248698},
	pmcid = {PMC3182649},
	keywords = {Animals, Brain Ischemia, Disease Models, Animal, Infarction, Middle Cerebral Artery, Mice, Middle Cerebral Artery, Silicon}
}

@article{endres_ischemia_2002,
	title = {Ischemia and stroke},
	volume = {513},
	issn = {0065-2598},
	doi = {10.1007/978-1-4615-0123-7_17},
	abstract = {Cell death following cerebral ischemia is mediated by a complex pathophysiologic interaction of different mechanisms. In this Chapter we will outline the basic principles as well as introduce in vitro and in vivo models of cerebral ischemia. Mechanistically, excitotoxicity, peri-infarct depolarization, inflammation and apoptosis seem to be the most relevant mediators of damage and are promising targets for neuroprotective strategies.},
	language = {eng},
	journal = {Advances in Experimental Medicine and Biology},
	author = {Endres, Matthias and Dirnagl, Ulrich},
	year = {2002},
	pmid = {12575832},
	keywords = {Acidosis, Animals, Apoptosis, Brain, Brain Ischemia, Caspase Inhibitors, Caspases, Disease Models, Animal, Humans, Inflammation, Necrosis, Receptors, Glutamate, Stroke, Temperature},
	pages = {455--473}
}

@article{crone_mice_2009,
	title = {In {Mice} {Lacking} {V}2a {Interneurons}, {Gait} {Depends} on {Speed} of {Locomotion}},
	volume = {29},
	copyright = {Copyright © 2009 Society for Neuroscience 0270-6474/09/297098-12\$15.00/0},
	issn = {0270-6474, 1529-2401},
	url = {https://www.jneurosci.org/content/29/21/7098},
	doi = {10.1523/JNEUROSCI.1206-09.2009},
	abstract = {Many animals are capable of changing gait with speed of locomotion. The neural basis of gait control and its dependence on speed are not fully understood. Mice normally use a single “trotting” gait while running at all speeds, either over ground or on a treadmill. Transgenic mouse mutants in which the trotting is replaced by hopping also lack a speed-dependent change in gait. Here we describe a transgenic mouse model in which the V2a interneurons have been ablated by targeted expression of diphtheria toxin A chain (DTA) under the control of the Chx10 gene promoter (Chx10::DTA mice). Chx10::DTA mice show normal trotting gait at slow speeds but transition to a galloping gait as speed increases. Although left–right limb coordination is altered in Chx10::DTA mice at fast speed, alternation of forelegs and hindlegs and the relative duration of swing and stance phases for individual limbs is unchanged compared with wild-type mice. The speed-dependent loss of left–right alternation is recapitulated during drug-induced fictive locomotion in spinal cords isolated from neonatal Chx10::DTA mice, and high-speed fictive locomotion evoked by caudal spinal cord stimulation also shows synchronous left–right bursting. These results show that spinal V2a interneurons are required for maintaining left–right alternation at high speeds. Whether animals that generate galloping or hopping gaits, characterized by synchronous movement of left and right forelegs and hindlegs, have lost or modified the function of V2a interneurons is an intriguing question.},
	language = {en},
	number = {21},
	urldate = {2019-07-28},
	journal = {Journal of Neuroscience},
	author = {Crone, Steven A. and Zhong, Guisheng and Harris-Warrick, Ronald and Sharma, Kamal},
	month = may,
	year = {2009},
	pmid = {19474336},
	pages = {7098--7109}
}

@article{solla_eliminating_1999,
	title = {Eliminating autocorrelation reduces biological relevance of home range estimates},
	volume = {68},
	issn = {1365-2656},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2656.1999.00279.x},
	doi = {10.1046/j.1365-2656.1999.00279.x},
	abstract = {1. Destructive subsampling or restrictive sampling are often standard procedures to obtain independence of spatial observations in home range analyses. We examined whether home range estimators based upon kernel densities require serial independence of observations, by using a Monte Carlo simulation, antler flies and snapping turtles as models. 2. Home range size, time partitioning and total straight line distances travelled were tested to determine if subsampling improved kernel performance and estimation of home range parameters. 3. The accuracy and precision of home range estimates from the simulated data set improved at shorter time intervals despite the increase in autocorrelation among the observations. 4. Subsampling did not reduce autocorrelation among locational observations of snapping turtles or antler flies, and home range size, time partitioning and total distance travelled were better represented by autocorrelated observations. 5. We found that kernel densities do not require serial independence of observations when estimating home range, and we recommend that researchers maximize the number of observations using constant time intervals to increase the accuracy and precision of their estimates.},
	language = {en},
	number = {2},
	urldate = {2021-02-13},
	journal = {Journal of Animal Ecology},
	author = {Solla, Shane R. DE and Bonduriansky, Russell and Brooks, Ronald J.},
	year = {1999},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2656.1999.00279.x},
	keywords = {Chelydra serpentina, Monte Carlo, Protopiophila litigata, kernel density estimation, statistical independence},
	pages = {221--234},
}

@article{bothe_genetic_2004,
	title = {Genetic and behavioral differences among five inbred mouse strains commonly used in the production of transgenic and knockout mice},
	volume = {3},
	issn = {1601-183X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1601-183x.2004.00064.x},
	doi = {10.1111/j.1601-183x.2004.00064.x},
	abstract = {Five strains of mice commonly used in transgenic and knockout production were compared with regard to genetic background and behavior. These strains were: C57BL/6J, C57BL/6NTac, 129P3/J (formerly 129/J), 129S6/SvEvTac (formerly 129/SvEvTac) and FVB/NTac. Genotypes for 342 microsatellite markers and performance in three behavioral tests (rotorod, open field activity and habituation, and contextual and cued fear conditioning) were determined. C57BL/6J and C57BL/6NTac were found to be true substrains; there were only 12 microsatellite differences between them. Given the data on the genetic background, one might predict that the two C57BL/6 substrains should be very similar behaviorally. Indeed, there were no significant behavioral differences between C57BL/6J and C57BL/6NTac. Contrary to literature reports on other 129 strains, 129S6/SvEvTac often performed similarly to C57BL/6 strains, except that it was less active. FVB/NTac showed impaired rotorod learning and cued fear conditioning. Therefore, both 129S6/SvEvTac and C57BL/6 are recommended as background strains for targeted mutations when researchers want to evaluate their mice in any of these three behavior tests. However, any transgene on the FVB/NTac background should be transferred to B6. Habituation to the open field was analyzed using the parameters: total distance, center distance, velocity and vertical activity. Contrary to earlier studies, we found that all strains habituated to the open field in at least two of these parameters (center distance and velocity).},
	language = {en},
	number = {3},
	urldate = {2019-07-28},
	journal = {Genes, Brain and Behavior},
	author = {Bothe, G. W. M. and Bolivar, V. J. and Vedder, M. J. and Geistfeld, J. G.},
	year = {2004},
	keywords = {Behavior, center avoidance, contextual and cued fear conditioning, genetics, habituation, inbred strain, leaning, microsatellite, motor coordination, mouse, open-field activity, rearing, rotorod},
	pages = {149--157}
}

@article{masocha_assessment_2009,
	title = {Assessment of weight bearing changes and pharmacological antinociception in mice with {LPS}-induced monoarthritis using the {Catwalk} gait analysis system},
	volume = {85},
	issn = {1879-0631},
	doi = {10.1016/j.lfs.2009.07.015},
	abstract = {AIMS: We evaluated the possibility of using the video-based Catwalk gait analysis method to measure weight bearing changes and for testing pharmacological antinociception in freely moving mice with lipopolysaccharide (LPS)-induced monoarthritis.
MAIN METHODS: LPS or its solvent (PBS) was injected intra-articularly into the right hind (RH) limb ankle joint through the Achilles tendon of C57BL/6 mice. The Catwalk system was used to assess behavioral changes in freely moving mice. The effects of indomethacin on changes in LPS-inoculated mice were examined.
KEY FINDINGS: Mice inoculated with LPS into the RH limb showed reduced paw pressure (measured as light intensity) and print area on the RH limb, whereas they exerted more pressure with the left hind (LH) and front limbs, showing a transfer of weight bearing from RH to LH and front limbs, which was significant at 2 days post-LPS inoculation. There were no differences between the front limbs. No changes were observed in the PBS injected controls. There were no changes in interlimb coordination (regularity index) in both PBS- and LPS-injected mice. Treatment with indomethacin (10 and 100mg/kg) restored the weight bearing (measured as the ratio of the pressure exerted by the paws) and the print area ratios of LPS-inoculated mice similar to that observed in control mice.
SIGNIFICANCE: This study shows that the Catwalk gait analysis system can be used to objectively quantify LPS-induced monoarthritis weight bearing changes in all four limbs and evaluate pharmacological antinociception in freely moving mice.},
	language = {eng},
	number = {11-12},
	journal = {Life Sciences},
	author = {Masocha, Willias and Parvathy, Subramanian S. and Pavarthy, Subramanian S.},
	month = sep,
	year = {2009},
	pmid = {19683012},
	keywords = {Achilles Tendon, Analgesics, Animals, Anti-Inflammatory Agents, Non-Steroidal, Arthritis, Experimental, Foot, Functional Laterality, Gait, Hindlimb, Indomethacin, Injections, Intra-Articular, Joints, Lighting, Lipopolysaccharides, Mice, Mice, Inbred C57BL, Weight-Bearing},
	pages = {462--469}
}

@article{hampton_gait_2004,
	title = {Gait dynamics in trisomic mice: quantitative neurological traits of {Down} syndrome},
	volume = {82},
	issn = {0031-9384},
	shorttitle = {Gait dynamics in trisomic mice},
	doi = {10.1016/j.physbeh.2004.04.006},
	abstract = {The segmentally trisomic mouse Ts65Dn is a model of Down syndrome (DS). Gait abnormalities are almost universal in persons with DS. We applied a noninvasive imaging method to quantitatively compare the gait dynamics of Ts65Dn mice (n=10) to their euploid littermates (controls) (n=10). The braking duration of the hind limbs in Ts65Dn mice was prolonged compared to that in control mice (60+/-3 ms vs. 49+/-2 ms, P{\textless}.05) at a slow walking speed (18 cm/s). Stride length and stride frequency of forelimbs and hind limbs were comparable between Ts65Dn mice and control mice. Stride dynamics were significantly different in Ts65Dn mice at a faster walking speed (36 cm/s). Stride length was shorter in Ts65Dn mice (5.9+/-0.1 vs. 6.3+/-0.3 cm, P{\textless}.05), and stride frequency was higher in Ts65Dn compared to control mice (5.9+/-0.1 vs. 5.3+/-0.1 strides/s, P{\textless}.05). Hind limb swing duration was prolonged in Ts65Dn mice compared to control mice (93+/-3 vs. 76+/-3 ms, P{\textless}.05). Propulsion of the forelimbs contributed to a significantly larger percentage of stride duration in Ts65Dn mice than in control mice at the faster walking speed. Indices of gait dynamics in Ts65Dn mice correspond to previously reported findings in children with DS. The methods used in the present study provide quantitative markers for genotype and phenotype relationship studies in DS. This technique may provide opportunities for testing the efficacy of therapies for motor dysfunction in persons with DS.},
	language = {eng},
	number = {2-3},
	journal = {Physiology \& Behavior},
	author = {Hampton, Thomas G. and Stasko, Melissa R. and Kale, Ajit and Amende, Ivo and Costa, Alberto C. S.},
	month = sep,
	year = {2004},
	pmid = {15276802},
	keywords = {Animals, Disease Models, Animal, Down Syndrome, Gait, Male, Mice, Mice, Neurologic Mutants, Motor Activity, Phenotype, Reference Values},
	pages = {381--389}
}

@article{parker_gait_1980,
	title = {Gait of children with {Down} syndrome},
	volume = {61},
	issn = {0003-9993},
	language = {eng},
	number = {8},
	journal = {Archives of Physical Medicine and Rehabilitation},
	author = {Parker, A. W. and Bronks, R.},
	month = aug,
	year = {1980},
	pmid = {6447490},
	keywords = {Child, Child Development, Down Syndrome, Female, Gait, Humans, Joints, Male, Muscle Contraction},
	pages = {345--351}
}

@article{amende_gait_2005,
	title = {Gait dynamics in mouse models of {Parkinson}'s disease and {Huntington}'s disease},
	volume = {2},
	issn = {1743-0003},
	doi = {10.1186/1743-0003-2-20},
	abstract = {BACKGROUND: Gait is impaired in patients with Parkinson's disease (PD) and Huntington's disease (HD), but gait dynamics in mouse models of PD and HD have not been described. Here we quantified temporal and spatial indices of gait dynamics in a mouse model of PD and a mouse model of HD.
METHODS: Gait indices were obtained in C57BL/6J mice treated with the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP, 30 mg/kg/day for 3 days) for PD, the mitochondrial toxin 3-nitropropionic acid (3NP, 75 mg/kg cumulative dose) for HD, or saline. We applied ventral plane videography to generate digital paw prints from which indices of gait and gait variability were determined. Mice walked on a transparent treadmill belt at a speed of 34 cm/s after treatments.
RESULTS: Stride length was significantly shorter in MPTP-treated mice (6.6 +/- 0.1 cm vs. 7.1 +/- 0.1 cm, P {\textless} 0.05) and stride frequency was significantly increased (5.4 +/- 0.1 Hz vs. 5.0 +/- 0.1 Hz, P {\textless} 0.05) after 3 administrations of MPTP, compared to saline-treated mice. The inability of some mice treated with 3NP to exhibit coordinated gait was due to hind limb failure while forelimb gait dynamics remained intact. Stride-to-stride variability was significantly increased in MPTP-treated and 3NP-treated mice compared to saline-treated mice. To determine if gait disturbances due to MPTP and 3NP, drugs affecting the basal ganglia, were comparable to gait disturbances associated with motor neuron diseases, we also studied gait dynamics in a mouse model of amyotrophic lateral sclerosis (ALS). Gait variability was not increased in the SOD1 G93A transgenic model of ALS compared to wild-type control mice.
CONCLUSION: The distinct characteristics of gait and gait variability in the MPTP model of Parkinson's disease and the 3NP model of Huntington's disease may reflect impairment of specific neural pathways involved.},
	language = {eng},
	journal = {Journal of Neuroengineering and Rehabilitation},
	author = {Amende, Ivo and Kale, Ajit and McCue, Scott and Glazier, Scott and Morgan, James P. and Hampton, Thomas G.},
	month = jul,
	year = {2005},
	pmid = {16042805},
	pmcid = {PMC1201165},
	pages = {20}
}

@incollection{jeung_mining_2007,
	address = {Berlin, Heidelberg},
	title = {Mining {Trajectory} {Patterns} {Using} {Hidden} {Markov} {Models}},
	volume = {4654},
	isbn = {978-3-540-74552-5 978-3-540-74553-2},
	url = {http://link.springer.com/10.1007/978-3-540-74553-2_44 https://espace.library.uq.edu.au/view/UQ:164937/MIC12UQ164937.pdf},
	booktitle = {Data {Warehousing} and {Knowledge} {Discovery}},
	publisher = {Springer Berlin Heidelberg},
	author = {Jeung, Hoyoung and Shen, Heng Tao and Zhou, Xiaofang},
	editor = {Song, Il Yeal and Eder, Johann and Nguyen, Tho Manh},
	year = {2007},
	note = {Type: Book Section},
	doi ={10.1007/978-3-540-74553-2_44},
	pages = {470--480},
}

@Article{         harris2020array,
 title         = {Array programming with {NumPy}},
 author        = {Charles R. Harris and K. Jarrod Millman and St{'{e}}fan J.
                 van der Walt and Ralf Gommers and Pauli Virtanen and David
                 Cournapeau and Eric Wieser and Julian Taylor and Sebastian
                 Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
                 and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
                 Brett and Allan Haldane and Jaime Fern{'{a}}ndez del
                 R{'{\i}}o and Mark Wiebe and Pearu Peterson and Pierre
                 G{'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
                 Travis E. Oliphant},
 year          = {2020},
 month         = sep,
 journal       = {Nature},
 volume        = {585},
 number        = {7825},
 pages         = {357--362},
 doi           = {10.1038/s41586-020-2649-2},
 publisher     = {Springer Science and Business Media {LLC}},
 url           = {https://doi.org/10.1038/s41586-020-2649-2}
}

@article{Waskom2021,
  doi = {10.21105/joss.03021},
  url = {https://doi.org/10.21105/joss.03021},
  year = {2021},
  publisher = {The Open Journal},
  volume = {6},
  number = {60},
  pages = {3021},
  author = {Michael L. Waskom},
  title = {seaborn: statistical data visualization},
  journal = {Journal of Open Source Software}
}

@Article{Hunter:2007,
  Author    = {Hunter, J. D.},
  Title     = {Matplotlib: A 2D graphics environment},
  Journal   = {Computing in Science \& Engineering},
  Volume    = {9},
  Number    = {3},
  Pages     = {90--95},
  abstract  = {Matplotlib is a 2D graphics package used for Python for
  application development, interactive scripting, and publication-quality
  image generation across user interfaces and operating systems.},
  publisher = {IEEE COMPUTER SOC},
  doi       = {10.1109/MCSE.2007.55},
  year      = 2007
}

@article{rowcliffe_bias_2012,
	title = {Bias in estimating animal travel distance: the effect of sampling frequency},
	volume = {3},
	copyright = {© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society},
	issn = {2041-210X},
	shorttitle = {Bias in estimating animal travel distance},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.2041-210X.2012.00197.x},
	doi = {10.1111/j.2041-210X.2012.00197.x},
	abstract = {1. The distance travelled by animals is an important ecological variable that links behaviour, energetics and demography. It is usually measured by summing straight-line distances between intermittently sampled locations along continuous animal movement paths. The extent to which this approach underestimates travel distance remains a rarely addressed and unsolved problem, largely because true movement paths are rarely, if ever, available for comparison. Here, we use simulated movement paths parameterized with empirical movement data to study how estimates of distance travelled are affected by sampling frequency. 2. We used a novel method to obtain fine-scale characteristics of animal movement from camera trap videos for a set of tropical forest mammals and used these characteristics to generate detailed movement paths. We then sampled these paths at different frequencies, simulating telemetry studies, and quantified the accuracy of sampled travel distance estimation. 3. For our focal species, typical telemetry studies would underestimate distances travelled by 67–93\%, and extremely high sampling frequencies (several fixes per minute) would be required to get tolerably accurate estimates. The form of the relationship between tortuosity, sample frequency, and distance travelled was such that absolute distance cannot accurately be estimated by the infrequent samples used in typical tracking studies. 4. We conclude that the underestimation of distance travelled is a serious but underappreciated problem. Currently, there is no reliable, widely applicable method to obtain approximately unbiased estimates of distance travelled by animals. Further research on this problem is needed.},
	language = {en},
	number = {4},
	urldate = {2021-02-14},
	journal = {Methods in Ecology and Evolution},
	author = {Rowcliffe, J. Marcus and Carbone, Chris and Kays, Roland and Kranstauber, Bart and Jansen, Patrick A.},
	year = {2012},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2012.00197.x},
	keywords = {Barro Colorado Island, camera traps, daily distance, day range, movement models, radiotracking, random walk, telemetry, travel distance, tropical forest},
	pages = {653--662},
}

@article{patterson_statistical_2017,
	title = {Statistical modelling of individual animal movement: an overview of key methods and a discussion of practical challenges},
	volume = {101},
	issn = {1863-818X},
	url = {https://doi.org/10.1007/s10182-017-0302-7},
	doi = {10.1007/s10182-017-0302-7},
	number = {4},
	journal = {AStA Advances in Statistical Analysis},
	author = {Patterson, Toby A. and Parton, Alison and Langrock, Roland and Blackwell, Paul G. and Thomas, Len and King, Ruth},
	year = {2017},
	note = {Type: Journal Article},
	pages = {399--438},
}

@article{morris_stride_1996,
	title = {Stride length regulation in {Parkinson}'s disease. {Normalization} strategies and underlying mechanisms},
	volume = {119 ( Pt 2)},
	issn = {0006-8950},
	doi = {10.1093/brain/119.2.551},
	abstract = {Results of our previous studies have shown that the slow, shuffling gait of Parkinson's disease patients is due to an inability to generate appropriate stride length and that cadence control is intact and is used as a compensatory mechanism. The reason for the reduced stride length is unclear, although deficient internal cue production or inadequate contribution to cortical motor set by the basal ganglia are two possible explanations. In this study we have examined the latter possibility by comparing the long-lasting effects of visual cues in improving stride length with that of attentional strategies. Computerized stride analysis was used to measure the spatial (distance) and temporal (timing) parameters of the walking pattern in a total of 54 subjects in three separate studies. In each study Parkinson's disease subjects were trained for 20 min by repeated 10 m walks set at control stride length (determined from control subjects matched for age, sex and height), using either visual floor markers or a mental picture of the appropriate stride size. Following training, the gait patterns were monitored (i) every 15 min for 2 h; (ii) whilst interspersing secondary tasks of increasing levels of complexity; (iii) covertly, when subjects were unaware that measurement was taking place. The results demonstrated that training with both visual cues and attentional strategies could maintain normal gait for the maximum recording time of 2 h. Secondary tasks reduced stride length towards baseline values as did covert monitoring. The findings confirm that the ability to generate a normal stepping pattern is not lost in Parkinson's disease and that gait hypokinesia reflects a difficulty in activating the motor control system. Normal stride length can be elicited in Parkinson's disease using attentional strategies and visual cues. Both strategies appear to share the same mechanism of focusing attention on the stride length. The effect of attention appears to require constant vigilance to prevent reverting to more automatic control mechanisms.},
	language = {eng},
	journal = {Brain: A Journal of Neurology},
	author = {Morris, M. E. and Iansek, R. and Matyas, T. A. and Summers, J. J.},
	month = apr,
	year = {1996},
	pmid = {8800948},
	keywords = {Aged, Aged, 80 and over, Attention, Cues, Female, Gait, Humans, Male, Middle Aged, Parkinson Disease, Time Factors},
	pages = {551--568}
}

@article{miller_locomotion_1975,
	title = {Locomotion in the cat: basic programmes of movement},
	volume = {91},
	issn = {0006-8993},
	shorttitle = {Locomotion in the cat},
	doi = {10.1016/0006-8993(75)90545-4},
	abstract = {Observations in cats of flexion and extension movements of the 4 limbs have led to the conclusion that the different forms of alternative locomotion (e.g. walking, trotting, swimming) and in-phase locomotion (galloping, jumping) result from the interaction of 'programmes' for the coordination of (1) the homologous limbs (pair of hindlimbs or pair of forelimbs) and (2) the homolateral limbs (hind- and forelimb of the same side of the body). The movements of the homologous pairs of limbs are coupled out of phase in alternate locomotion and approximately in phase in the phase form of locomotion. The movements of the homolateral pairs of limbs occur approximately out of phase in the trotting type of coupling and approximately in phase in the pacing type of coupling. Transitions between the different forms of coupling occur abruptly over 1 or 2 steps. Therefore, for each type of coupling (homologous or homolateral) there are two distinct forms or 'programmes' of movement. The hypothesis is advanced that (a) all the characteristic patterns of locomotion in the cat result from different combinations of these 'programmes' of homologous and homolateral limb coupling; (b) the 'programmes' are mutually self reinforcing in the gaits in which the coordination of the movements of the 4 limbs is bilaterally symmetrical; (c) the 'programmes' act in competition in certain gaits which are not bilaterally symmetrical giving rise at times to a changing gait pattern, and (d) the temporary dominance of one 'programme' or another can determine the gait of the particular step.},
	language = {eng},
	number = {2},
	journal = {Brain Research},
	author = {Miller, S. and Van Der Burg, J. and Van Der Meché, F.},
	month = jun,
	year = {1975},
	pmid = {1080684},
	keywords = {5-Hydroxytryptophan, Animals, Cats, Clonidine, Decerebrate State, Forelimb, Gait, Hindlimb, Levodopa, Movement, Spinal Cord, Swimming},
	pages = {239--253}
}

@article{morris_gait_2001,
	title = {Gait disorders and gait rehabilitation in {Parkinson}'s disease},
	volume = {87},
	issn = {0091-3952},
	language = {eng},
	journal = {Advances in Neurology},
	author = {Morris, M. E. and Huxham, F. E. and McGinley, J. and Iansek, R.},
	year = {2001},
	pmid = {11347239},
	keywords = {Biomechanical Phenomena, Gait, Gait Disorders, Neurologic, Humans, Parkinson Disease},
	pages = {347--361}
}

@article{barriere_prominent_2008,
	title = {Prominent role of the spinal central pattern generator in the recovery of locomotion after partial spinal cord injuries},
	volume = {28},
	issn = {1529-2401},
	doi = {10.1523/JNEUROSCI.5692-07.2008},
	abstract = {The re-expression of hindlimb locomotion after complete spinal cord injuries (SCIs) is caused by the presence of a spinal central pattern generator (CPG) for locomotion. After partial SCI, however, the role of this spinal CPG in the recovery of hindlimb locomotion in the cat remains mostly unknown. In the present work, we devised a dual-lesion paradigm to determine its possible contribution after partial SCI. After a partial section of the left thoracic segment T10 or T11, cats gradually recovered voluntary quadrupedal locomotion. Then, a complete transection was performed two to three segments more caudally (T13-L1) several weeks after the first partial lesion. Cats that received intensive treadmill training after the partial lesion expressed bilateral hindlimb locomotion within hours of the complete lesion. Untrained cats however showed asymmetrical hindlimb locomotion with the limb on the side of the partial lesion walking well before the other hindlimb. Thus, the complete spinalization revealed that the spinal CPG underwent plastic changes after the partial lesions, which were shaped by locomotor training. Over time, with further treadmill training, the asymmetry disappeared and a bilateral locomotion was reinstated. Therefore, although remnant intact descending pathways must contribute to voluntary goal-oriented locomotion after partial SCI, the recovery and re-expression of the hindlimb locomotor pattern mostly results from intrinsic changes below the lesion in the CPG and afferent inputs.},
	language = {eng},
	number = {15},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Barrière, Grégory and Leblond, Hugues and Provencher, Janyne and Rossignol, Serge},
	month = apr,
	year = {2008},
	pmid = {18400897},
	keywords = {Animals, Cats, Extremities, Female, Lumbar Vertebrae, Male, Motor Activity, Neuronal Plasticity, Physical Conditioning, Animal, Recovery of Function, Spinal Cord, Spinal Cord Injuries, Thoracic Vertebrae},
	pages = {3976--3987}
}

@article{cascallares_role_2018,
	title = {Role of the circadian clock in the statistics of locomotor activity in {Drosophila}.},
	volume = {13},
	url = {http://dx.doi.org/10.1371/journal.pone.0202505},
	doi = {10.1371/journal.pone.0202505},
	abstract = {In many animals the circadian rhythm of locomotor activity is controlled by an endogenous circadian clock. Using custom made housing and video tracking software in order to obtain high spatial and temporal resolution, we studied the statistical properties of the locomotor activity of wild type and two clock mutants of Drosophila melanogaster. We show here that the distributions of activity and quiescence bouts for the clock mutants in light-dark conditions (LD) are very different from the distributions obtained when there are no external cues from the environment (DD). In the wild type these distributions are very similar, showing that the clock controls this aspect of behavior in both regimes (LD and DD). Furthermore, the distributions are very similar to those reported for Wistar rats. For the timing of events we also observe important differences, quantified by how the event rate distributions scale for increasing time windows. We find that for the wild type these distributions can be rescaled by the same function in DD as in LD. Interestingly, the same function has been shown to rescale the rate distributions in Wistar rats. On the other hand, for the clock mutants it is not possible to rescale the rate distributions, which might indicate that the extent of circadian control depends on the statistical properties of activity and quiescence.},
	number = {8},
	urldate = {2019-07-12},
	journal = {Plos One},
	author = {Cascallares, Guadalupe and Riva, Sabrina and Franco, D Lorena and Risau-Gusman, Sebastian and Gleiser, Pablo M},
	month = aug,
	year = {2018},
	pmid = {30138403},
	pmcid = {PMC6107170},
	pages = {e0202505}
}

@book{batschelet_circular_1981,
	address = {London},
	title = {Circular {Statistics} {In} {Biology} (mathematics {In} {Biology})},
	isbn = {0-12-081050-6},
	urldate = {2019-07-12},
	publisher = {Academic Press},
	author = {Batschelet, Edward},
	year = {1981}
}

@article{wiesmann_specific_2017,
	title = {A specific dietary intervention to restore brain structure and function after ischemic stroke.},
	volume = {7},
	url = {http://dx.doi.org/10.7150/thno.17559},
	doi = {10.7150/thno.17559},
	abstract = {Occlusion of the middle cerebral artery (MCAo) is among the most common causes of ischemic stroke in humans. Cerebral ischemia leads to brain lesions existing of an irreversibly injured core and an ischemic boundary zone, the penumbra, containing damaged but potentially salvageable tissue. Using a transient occlusion (30 min) of the middle cerebral artery (tMCAo) mouse model in this cross-institutional study we investigated the neurorestorative efficacy of a dietary approach (Fortasyn) comprising docosahexaenoic acid, eicosapentaenoic acid, uridine, choline, phospholipids, folic acid, vitamins B12, B6, C, and E, and selenium as therapeutic approach to counteract neuroinflammation and impairments of cerebral (structural+functional) connectivity, cerebral blood flow (CBF), and motor function. Male adult C57BL/6j mice were subjected to right tMCAo using the intraluminal filament model. Following tMCAo, animals were either maintained on Control diet or switched to the multicomponent Fortasyn diet. At several time points after tMCAo, behavioral tests, and MRI and PET scanning were conducted to identify the impact of the multicomponent diet on the elicited neuroinflammatory response, loss of cerebral connectivity, and the resulting impairment of motor function after experimental stroke. Mice on the multicomponent diet showed decreased neuroinflammation, improved functional and structural connectivity, beneficial effect on CBF, and also improved motor function after tMCAo. Our present data show that this specific dietary intervention may have beneficial effects on structural and functional recovery and therefore therapeutic potential after ischemic stroke.},
	number = {2},
	urldate = {2019-03-14},
	journal = {Theranostics},
	author = {Wiesmann, Maximilian and Zinnhardt, Bastian and Reinhardt, Dirk and Eligehausen, Sarah and Wachsmuth, Lydia and Hermann, Sven and Dederen, Pieter J and Hellwich, Marloes and Kuhlmann, Michael T and Broersen, Laus M and Heerschap, Arend and Jacobs, Andreas H and Kiliaan, Amanda J},
	month = jan,
	year = {2017},
	pmid = {28255345},
	pmcid = {PMC5327363},
	pages = {493--512}
}

@article{benjamini_ten_2010,
	title = {Ten ways to improve the quality of descriptions of whole-animal movement.},
	volume = {34},
	url = {http://dx.doi.org/10.1016/j.neubiorev.2010.04.004},
	doi = {10.1016/j.neubiorev.2010.04.004},
	abstract = {The demand for replicability of behavioral results across laboratories is viewed as a burden in behavior genetics. We demonstrate how it can become an asset offering a quantitative criterion that guides the design of better ways to describe behavior. Passing the high benchmark dictated by the replicability demand requires less stressful and less restraining experimental setups, less noisy data, individually customized cutoff points between the building blocks of movement, and less variable yet discriminative dynamic representations that would capture more faithfully the nature of the behavior, unmasking similarities and differences and revealing novel animal-centered measures. Here we review ten tools that enhance replicability without compromising discrimination. While we demonstrate the usefulness of these tools in the context of inbred mouse exploratory behavior they can readily be used in any study involving a high-resolution analysis of spatial behavior. Viewing replicability as a design concept and using the ten methodological improvements may prove useful in many fields not necessarily related to spatial behavior.},
	number = {8},
	urldate = {2019-03-11},
	journal = {Neuroscience and Biobehavioral Reviews},
	author = {Benjamini, Yoav and Lipkind, Dina and Horev, Guy and Fonio, Ehud and Kafkafi, Neri and Golani, Ilan},
	month = jul,
	year = {2010},
	pmid = {20399806},
	pages = {1351--1365}
}

@article{maier_big_2017,
	title = {Big data in large-scale systemic mouse phenotyping},
	volume = {4},
	issn = {24523100},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2452310017300525},
	doi = {10.1016/j.coisb.2017.07.012},
	abstract = {Systemic phenotyping of mutant mice has been established at large scale in the last decade as a new tool to uncover the relations between genotype, phenotype and environment. Recent advances in that field led to the generation of a valuable open access data resource that can be used to better understanding the underlying causes for human diseases. From an ethical perspective, systemic phenotyping significantly contributes to the reduction of experimental animals and the refinement of animal experiments by enforcing standardisation efforts. There are particular logistical, experimental and analytical challenges of systemic large-scale mouse phenotyping. On all levels, IT solutions are critical to implement and efficiently support breeding, phenotyping and data analysis processes that lead to the generation of high-quality systemic phenotyping data accessible for the scientific community.},
	urldate = {2019-01-13},
	journal = {Current Opinion in Systems Biology},
	author = {Maier, Holger and Leuchtenberger, Stefanie and Fuchs, Helmut and Gailus-Durner, Valerie and Hrabe de Angelis, Martin},
	month = aug,
	year = {2017},
	pages = {97--104}
}

@article{wiesmann_effect_2018,
	title = {Effect of a multinutrient intervention after ischemic stroke in female {C}57Bl/6 mice.},
	volume = {144},
	url = {http://dx.doi.org/10.1111/jnc.14213},
	doi = {10.1111/jnc.14213},
	abstract = {Stroke can affect females very differently from males, and therefore preclinical research on underlying mechanisms and the effects of interventions should not be restricted to male subjects, and treatment strategies for stroke should be tailored to benefit both sexes. Previously, we demonstrated that a multinutrient intervention (Fortasyn) improved impairments after ischemic stroke induction in male C57Bl/6 mice, but the therapeutic potential of this dietary treatment remained to be investigated in females. We now induced a transient middle cerebral artery occlusion (tMCAo) in C57Bl/6 female mice and immediately after surgery switched to either Fortasyn or an isocaloric Control diet. The stroke females performed several behavioral and motor tasks before and after tMCAo and were scanned in an 11.7 Tesla magnetic resonance imaging (MRI) scanner to assess brain perfusion, integrity, and functional connectivity. To assess brain plasticity, inflammation, and vascular integrity, immunohistochemistry was performed after killing of the mice. We found that the multinutrient intervention had diverse effects on the stroke-induced impairments in females. Similar to previous observations in male stroke mice, brain integrity, sensorimotor integration and neurogenesis benefitted from Fortasyn, but impairments in activity and motor skills were not improved in female stroke mice. Overall, Fortasyn effects in the female stroke mice seem more modest in comparison to previously investigated male stroke mice. We suggest that with further optimization of treatment protocols more information on the efficacy of specific interventions in stroked females can be gathered. This in turn will help with the development of (gender-specific) treatment regimens for cerebrovascular diseases such as stroke. This article is part of the Special Issue "Vascular Dementia". {\textbackslash}copyright 2017 International Society for Neurochemistry.},
	number = {5},
	urldate = {2019-01-13},
	journal = {Journal of Neurochemistry},
	author = {Wiesmann, Maximilian and Timmer, Nienke M and Zinnhardt, Bastian and Reinhard, Dirk and Eligehausen, Sarah and Königs, Anja and Ben Jeddi, Hasnae and Dederen, Pieter J and Jacobs, Andreas H and Kiliaan, Amanda J},
	month = mar,
	year = {2018},
	pmid = {28888042},
	pages = {549--564}
}

@article{zheng_trajectory_2015,
	title = {Trajectory {Data} {Mining}},
	volume = {6},
	issn = {21576904},
	url = {http://dl.acm.org/citation.cfm?doid=2764959.2743025},
	doi = {10.1145/2743025},
	abstract = {The advances in location-acquisition and mobile computing techniques have generated massive spatial trajectory data, which represent the mobility of a diversity of moving objects, such as people, vehicles, and animals. Many techniques have been proposed for processing, managing, and mining trajectory data in the past decade, fostering a broad range of applications. In this article, we conduct a systematic survey on the major research into trajectory data mining , providing a panorama of the field as well as the scope of its research topics. Following a road map from the derivation of trajectory data, to trajectory data preprocessing, to trajectory data management, and to a variety of mining tasks (such as trajectory pattern mining, outlier detection, and trajectory classification), the survey explores the connections, correlations, and differences among these existing techniques. This survey also introduces the methods that transform trajectories into other data formats, such as graphs, matrices, and tensors, to which more data mining and machine learning techniques can be applied. Finally, some public trajectory datasets are presented. This survey can help shape the field of trajectory data mining , providing a quick understanding of this field to the community.},
	number = {3},
	urldate = {2019-03-23},
	journal = {ACM transactions on intelligent systems and technology},
	author = {Zheng, Yu},
	month = may,
	year = {2015},
	pages = {1--41}
}

@article{valletta_applications_2017,
	title = {Applications of machine learning in animal behaviour studies},
	volume = {124},
	issn = {00033472},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0003347216303360},
	doi = {10.1016/j.anbehav.2016.12.005},
	abstract = {Highlights•Machine learning (ML) offers a hypothesis-free approach to modelling complex data.•We present a review of ML techniques pertinent to the study of animal behaviour.•Key ML approaches are illustrated using three different case studies.•ML offers a useful addition to the animal behaviourist's analytical toolbox. In many areas of animal behaviour research, improvements in our ability to collect large and detailed data sets are outstripping our ability to analyse them. These diverse, complex and often high-dimensional data sets exhibit nonlinear dependencies and unknown interactions across multiple variables, and may fail to conform to the assumptions of many classical statistical methods. The field of machine learning provides methodologies that are ideally suited to the task of extracting knowledge from these data. In this review, we aim to introduce animal behaviourists unfamiliar with machine learning (ML) to the promise of these techniques for the analysis of complex behavioural data. We start by describing the rationale behind ML and review a number of animal behaviour studies where ML has been successfully deployed. The ML framework is then introduced by presenting several unsupervised and supervised learning methods. Following this overview, we illustrate key ML approaches by developing data analytical pipelines for three different case studies that exemplify the types of behavioural and ecological questions ML can address. The first uses a large number of spectral and morphological characteristics that describe the appearance of pheasant, Phasianus colchicus, eggs to assign them to putative clutches. The second takes a continuous data stream of feeder visits from PIT (passive integrated transponder)-tagged jackdaws, Corvus monedula, and extracts foraging events from it, which permits the construction of social networks. Our final example uses aerial images to train a classifier that detects the presence of wildebeest, Connochaetes taurinus, to count individuals in a population. With the advent of cheaper sensing and tracking technologies an unprecedented amount of data on animal behaviour is becoming available. We believe that ML will play a central role in translating these data into scientific knowledge and become a useful addition to the animal behaviourist's analytical toolkit.},
	urldate = {2019-07-12},
	journal = {Animal Behaviour},
	author = {Valletta, John Joseph and Torney, Colin and Kings, Michael and Thornton, Alex and Madden, Joah},
	month = feb,
	year = {2017},
	pages = {203--220}
}

@article{brown_compass:_2016,
	title = {{COMPA}{\textbackslash}{SS}: continuous open mouse phenotyping of activity and sleep status.},
	volume = {1},
	url = {http://dx.doi.org/10.12688/wellcomeopenres.9892.2},
	doi = {10.12688/wellcomeopenres.9892.2},
	abstract = {Background Disruption of rhythms in activity and rest occur in many diseases, and provide an important indicator of healthy physiology and behaviour. However, outside the field of sleep and circadian rhythm research, these rhythmic processes are rarely measured due to the requirement for specialised resources and expertise. Until recently, the primary approach to measuring activity in laboratory rodents has been based on voluntary running wheel activity. By contrast, measuring sleep requires the use of electroencephalography (EEG), which involves invasive surgical procedures and time-consuming data analysis. Methods Here we describe a simple, non-invasive system to measure home cage activity in mice based upon passive infrared (PIR) motion sensors. Careful calibration of this system will allow users to simultaneously assess sleep status in mice. The use of open-source tools and simple sensors keeps the cost and the size of data-files down, in order to increase ease of use and uptake. Results In addition to providing accurate data on circadian activity parameters, here we show that extended immobility of {\textbackslash}textgreater40 seconds provides a reliable indicator of sleep, correlating well with EEG-defined sleep (Pearson's r {\textbackslash}textgreater0.95, 4 mice). Conclusions Whilst any detailed analysis of sleep patterns in mice will require EEG, behaviourally-defined sleep provides a valuable non-invasive means of simultaneously phenotyping both circadian rhythms and sleep. Whilst previous approaches have relied upon analysis of video data, here we show that simple motion sensors provide a cheap and effective alternative, enabling real-time analysis and longitudinal studies extending over weeks or even months. The data files produced are small, enabling easy deposition and sharing. We have named this system COMPA{\textbackslash}SS - Continuous Open Mouse Phenotyping of Activity and Sleep Status. This simple approach is of particular value in phenotyping screens as well as providing an ideal tool to assess activity and rest cycles for non-specialists.},
	urldate = {2019-03-14},
	journal = {Wellcome Open Research},
	author = {Brown, Laurence A and Hasan, Sibah and Foster, Russell G and Peirson, Stuart N},
	month = nov,
	year = {2016},
	pmid = {27976750},
	pmcid = {PMC5140024},
	pages = {2}
}

@article{dickinson_high-throughput_2016,
	title = {High-throughput discovery of novel developmental phenotypes.},
	volume = {537},
	url = {http://dx.doi.org/10.1038/nature19356},
	doi = {10.1038/nature19356},
	abstract = {Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.},
	number = {7621},
	urldate = {2018-02-07},
	journal = {Nature},
	author = {Dickinson, Mary E and Flenniken, Ann M and Ji, Xiao and Teboul, Lydia and Wong, Michael D and White, Jacqueline K and Meehan, Terrence F and Weninger, Wolfgang J and Westerberg, Henrik and Adissu, Hibret and Baker, Candice N and Bower, Lynette and Brown, James M and Caddle, L Brianna and Chiani, Francesco and Clary, Dave and Cleak, James and Daly, Mark J and Denegre, James M and Doe, Brendan and Dolan, Mary E and Edie, Sarah M and Fuchs, Helmut and Gailus-Durner, Valerie and Galli, Antonella and Gambadoro, Alessia and Gallegos, Juan and Guo, Shiying and Horner, Neil R and Hsu, Chih-Wei and Johnson, Sara J and Kalaga, Sowmya and Keith, Lance C and Lanoue, Louise and Lawson, Thomas N and Lek, Monkol and Mark, Manuel and Marschall, Susan and Mason, Jeremy and McElwee, Melissa L and Newbigging, Susan and Nutter, Lauryl M J and Peterson, Kevin A and Ramirez-Solis, Ramiro and Rowland, Douglas J and Ryder, Edward and Samocha, Kaitlin E and Seavitt, John R and Selloum, Mohammed and Szoke-Kovacs, Zsombor and Tamura, Masaru and Trainor, Amanda G and Tudose, Ilinca and Wakana, Shigeharu and Warren, Jonathan and Wendling, Olivia and West, David B and Wong, Leeyean and Yoshiki, Atsushi and Consortium, International Mouse Phenotyping and Laboratory, Jackson and Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS) and Laboratories, Charles River and Harwell, M. R. C. and Phenogenomics, Toronto Centre for and Institute, Wellcome Trust Sanger and Center, RIKEN BioResource and MacArthur, Daniel G and Tocchini-Valentini, Glauco P and Gao, Xiang and Flicek, Paul and Bradley, Allan and Skarnes, William C and Justice, Monica J and Parkinson, Helen E and Moore, Mark and Wells, Sara and Braun, Robert E and Svenson, Karen L and de Angelis, Martin Hrabe and Herault, Yann and Mohun, Tim and Mallon, Ann-Marie and Henkelman, R Mark and Brown, Steve D M and Adams, David J and Lloyd, K C Kent and McKerlie, Colin and Beaudet, Arthur L and Bućan, Maja and Murray, Stephen A},
	month = sep,
	year = {2016},
	pmid = {27626380},
	pmcid = {PMC5295821},
	pages = {508--514}
}

@article{pack_novel_2007,
	title = {Novel method for high-throughput phenotyping of sleep in mice.},
	volume = {28},
	url = {http://dx.doi.org/10.1152/physiolgenomics.00139.2006},
	doi = {10.1152/physiolgenomics.00139.2006},
	abstract = {Assessment of sleep in mice currently requires initial implantation of chronic electrodes for assessment of electroencephalogram (EEG) and electromyogram (EMG) followed by time to recover from surgery. Hence, it is not ideal for high-throughput screening. To address this deficiency, a method of assessment of sleep and wakefulness in mice has been developed based on assessment of activity/inactivity either by digital video analysis or by breaking infrared beams in the mouse cage. It is based on the algorithm that any episode of continuous inactivity of {\textbackslash}textgreater or =40 s is predicted to be sleep. The method gives excellent agreement in C57BL/6J male mice with simultaneous assessment of sleep by EEG/EMG recording. The average agreement over 8,640 10-s epochs in 24 h is 92\% (n = 7 mice) with agreement in individual mice being 88-94\%. Average EEG/EMG determined sleep per 2-h interval across the day was 59.4 min. The estimated mean difference (bias) per 2-h interval between inactivity-defined sleep and EEG/EMG-defined sleep was only 1.0 min (95\% confidence interval for mean bias -0.06 to +2.6 min). The standard deviation of differences (precision) was 7.5 min per 2-h interval with 95\% limits of agreement ranging from -13.7 to +15.7 min. Although bias significantly varied by time of day (P = 0.0007), the magnitude of time-of-day differences was not large (average bias during lights on and lights off was +5.0 and -3.0 min per 2-h interval, respectively). This method has applications in chemical mutagenesis and for studies of molecular changes in brain with sleep/wakefulness.},
	number = {2},
	urldate = {2019-03-14},
	journal = {Physiological Genomics},
	author = {Pack, Allan I and Galante, Raymond J and Maislin, Greg and Cater, Jacqueline and Metaxas, Dimitris and Lu, Shan and Zhang, Lin and Von Smith, Randy and Kay, Timothy and Lian, Jie and Svenson, Karen and Peters, Luanne L},
	month = jan,
	year = {2007},
	pmid = {16985007},
	pages = {232--238}
}

@article{eckel-mahan_phenotyping_2015,
	title = {Phenotyping circadian rhythms in mice.},
	volume = {5},
	url = {http://dx.doi.org/10.1002/9780470942390.mo140229},
	doi = {10.1002/9780470942390.mo140229},
	abstract = {Circadian rhythms take place with a periodicity of 24 hr, temporally following the rotation of the earth around its axis. Examples of circadian rhythms are the sleep/wake cycle, feeding, and hormone secretion. Light powerfully entrains the mammalian clock and assists in keeping animals synchronized to the 24-hour cycle of the earth by activating specific neurons in the "central pacemaker" of the brain, the suprachiasmatic nucleus. Absolute periodicity of an animal can deviate slightly from 24 hr as manifest when an animal is placed into constant dark or "free-running" conditions. Simple measurements of an organism's activity in free-running conditions reveal its intrinsic circadian period. Mice are a particularly useful model for studying circadian rhythmicity due to the ease of genetic manipulation, thus identifying molecular contributors to rhythmicity. Furthermore, their small size allows for monitoring locomotion or activity in their homecage environment with relative ease. Several tasks commonly used to analyze circadian periodicity and plasticity in mice are presented here including the process of entrainment, determination of tau (period length) in free-running conditions, determination of circadian periodicity in response to light disruption (e.g., jet lag studies), and evaluation of clock plasticity in non-24-hour conditions (T-cycles). Studying the properties of circadian periods such as their phase, amplitude, and length in response to photic perturbation, can be particularly useful in understanding how humans respond to jet lag, night shifts, rotating shifts, or other transient or chronic disruption of environmental surroundings. Copyright {\textbackslash}copyright 2015 John Wiley \& Sons, Inc.},
	number = {3},
	urldate = {2019-03-15},
	journal = {Current protocols in mouse biology},
	author = {Eckel-Mahan, Kristin and Sassone-Corsi, Paolo},
	month = sep,
	year = {2015},
	pmid = {26331760},
	pmcid = {PMC4732881},
	pages = {271--281}
}

@article{rosenthal_mouse_2007,
	title = {The mouse ascending: perspectives for human-disease models.},
	volume = {9},
	url = {http://dx.doi.org/10.1038/ncb437},
	doi = {10.1038/ncb437},
	abstract = {The laboratory mouse is widely considered the model organism of choice for studying the diseases of humans, with whom they share 99\% of their genes. A distinguished history of mouse genetic experimentation has been further advanced by the development of powerful new tools to manipulate the mouse genome. The recent launch of several international initiatives to analyse the function of all mouse genes through mutagenesis, molecular analysis and phenotyping underscores the utility of the mouse for translating the information stored in the human genome into increasingly accurate models of human disease.},
	number = {9},
	urldate = {2019-01-12},
	journal = {Nature Cell Biology},
	author = {Rosenthal, Nadia and Brown, Steve},
	month = sep,
	year = {2007},
	pmid = {17762889},
	pages = {993--999}
}

@article{noldus_ethovision:_2001,
	title = {{EthoVision}: a versatile video tracking system for automation of behavioral experiments.},
	volume = {33},
	url = {http://dx.doi.org/10.3758/BF03195394},
	doi = {10.3758/BF03195394},
	abstract = {The need for automating behavioral observations and the evolution of systems developed for that purpose is outlined. Video tracking systems enable researchers to study behavior in a reliable and consistent way and over longer time periods than if they were using manual recording. To overcome limitations of currently available systems, we have designed EthoVision, an integrated system for automatic recording of activity, movement, and interactions of animals. The EthoVision software is presented, highlighting some key features that separate EthoVision from other systems: easy file management, independent variable definition, flexible arena and zone design, several methods of data acquisition allowing identification and tracking of multiple animals in multiple arenas, and tools for visualization of the tracks and calculation of a range of analysis parameters. A review of studies using EthoVision is presented, demonstrating the system's use in a wide variety of applications. Possible future directions for development are discussed.},
	number = {3},
	urldate = {2019-07-12},
	journal = {Behavior research methods, instruments, \& computers : a journal of the Psychonomic Society, Inc},
	author = {Noldus, L P and Spink, A J and Tegelenbosch, R A},
	month = aug,
	year = {2001},
	pmid = {11591072},
	pages = {398--414}
}

@article{goulding_robust_2008,
	title = {A robust automated system elucidates mouse home cage behavioral structure.},
	volume = {105},
	issn = {1091-6490},
	url = {http://dx.doi.org/10.1073/pnas.0809053106},
	doi = {10.1073/pnas.0809053106},
	abstract = {Patterns of behavior exhibited by mice in their home cages reflect the function and interaction of numerous behavioral and physiological systems. Detailed assessment of these patterns thus has the potential to provide a powerful tool for understanding basic aspects of behavioral regulation and their perturbation by disease processes. However, the capacity to identify and examine these patterns in terms of their discrete levels of organization across diverse behaviors has been difficult to achieve and automate. Here, we describe an automated approach for the quantitative characterization of fundamental behavioral elements and their patterns in the freely behaving mouse. We demonstrate the utility of this approach by identifying unique features of home cage behavioral structure and changes in distinct levels of behavioral organization in mice with single gene mutations altering energy balance. The robust, automated, reproducible quantification of mouse home cage behavioral structure detailed here should have wide applicability for the study of mammalian physiology, behavior, and disease.},
	number = {52},
	urldate = {2019-03-11},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Goulding, Evan H and Schenk, A Katrin and Juneja, Punita and MacKay, Adrienne W and Wade, Jennifer M and Tecott, Laurence H},
	month = dec,
	year = {2008},
	pmid = {19106295},
	pmcid = {PMC2634928},
	pages = {20575--20582}
}

@article{jhuang_automated_2010,
	title = {Automated home-cage behavioural phenotyping of mice.},
	volume = {1},
	url = {http://dx.doi.org/10.1038/ncomms1064},
	doi = {10.1038/ncomms1064},
	abstract = {Neurobehavioural analysis of mouse phenotypes requires the monitoring of mouse behaviour over long periods of time. In this study, we describe a trainable computer vision system enabling the automated analysis of complex mouse behaviours. We provide software and an extensive manually annotated video database used for training and testing the system. Our system performs on par with human scoring, as measured from ground-truth manual annotations of thousands of clips of freely behaving mice. As a validation of the system, we characterized the home-cage behaviours of two standard inbred and two non-standard mouse strains. From these data, we were able to predict in a blind test the strain identity of individual animals with high accuracy. Our video-based software will complement existing sensor-based automated approaches and enable an adaptable, comprehensive, high-throughput, fine-grained, automated analysis of mouse behaviour.},
	urldate = {2019-03-11},
	journal = {Nature Communications},
	author = {Jhuang, Hueihan and Garrote, Estibaliz and Mutch, Jim and Yu, Xinlin and Khilnani, Vinita and Poggio, Tomaso and Steele, Andrew D and Serre, Thomas},
	month = sep,
	year = {2010},
	pmid = {20842193},
	pages = {68}
}

@article{casadesus_automated_2001,
	title = {Automated measurement of age-related changes in the locomotor response to environmental novelty and home-cage activity.},
	volume = {122},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/11557287},
	abstract = {The likelihood to explore in an open-field environment decreases with age. Older animals tend to be less active and explore less both in novel and home-cage environments. The locomotor performance (fine movements, ambulatory movements, and rearing) of male Fischer 344 (F344) rats that were 6 (n=6) or 22 (n=6) months of age was evaluated by continuous automated counting of photobeam interruptions, every 30 min, during 60 consecutive hours, in standard polycarbonate cages. Novel environment performance was determined by photobeam interruption counting during the first hour in the new cage. The remaining 59 h were evaluated as home-cage activity. A significant age-related decrease in ambulatory and fine motor activity was seen during the first hour of testing (novel environment). In addition, aged rats showed a decreased number of ambulatory and fine movements in home-cage activity, predominantly during the dark portion of the light cycle and during or around both light-switch periods (05:00 and 17:00). No differences were seen in rearing behavior. These findings provide a more detailed analysis and additional evidence of the activity decreases and rhythmic changes seen in aged F344 rats under uninterrupted testing conditions.},
	number = {15},
	urldate = {2019-07-12},
	journal = {Mechanisms of Ageing and Development},
	author = {Casadesus, G and Shukitt-Hale, B and Joseph, J A},
	month = oct,
	year = {2001},
	pmid = {11557287},
	pages = {1887--1897},
	doi ={10.1016/s0047-6374(01)00324-4 },
}

@article{crawley_behavioral_2008,
	title = {Behavioral phenotyping strategies for mutant mice.},
	volume = {57},
	url = {http://dx.doi.org/10.1016/j.neuron.2008.03.001},
	doi = {10.1016/j.neuron.2008.03.001},
	abstract = {Comprehensive behavioral analyses of transgenic and knockout mice have successfully identified the functional roles of many genes in the brain. Over the past 10 years, strategies for mouse behavioral phenotyping have evolved to maximize the scope and replicability of findings from a cohort of mutant mice, minimize the interpretation of procedural artifacts, and provide robust translational tools to test hypotheses and develop treatments. This Primer addresses experimental design issues and offers examples of high-throughput batteries, learning and memory tasks, and anxiety-related tests.},
	number = {6},
	urldate = {2019-03-14},
	journal = {Neuron},
	author = {Crawley, Jacqueline N},
	month = mar,
	year = {2008},
	pmid = {18367082},
	pages = {809--818}
}

@article{tester_arm_2012,
	title = {Arm and leg coordination during treadmill walking in individuals with motor incomplete spinal cord injury: a preliminary study.},
	volume = {36},
	url = {http://dx.doi.org/10.1016/j.gaitpost.2012.01.004},
	doi = {10.1016/j.gaitpost.2012.01.004},
	abstract = {Arm and leg coordination naturally emerges during walking, but can be affected by stroke or Parkinson's disease. The purpose of this preliminary study was to characterize arm and leg coordination during treadmill walking at self-selected comfortable walking speeds (CWSs) in individuals using arm swing with motor incomplete spinal cord injury (iSCI). Hip and shoulder angle cycle durations and amplitudes, strength of peak correlations between contralateral hip and shoulder joint angle time series, the time shifts at which these peak correlations occur, and associated variability were quantified. Outcomes in individuals with iSCI selecting fast CWSs (range, 1.0-1.3m/s) and speed-matched individuals without neurological injuries are similar. Differences, however, are detected in individuals with iSCI selecting slow CWSs (range, 0.25-0.65 m/s) and may represent compensatory strategies to improve walking balance or forward propulsion. These individuals elicit a 1:1, arm:leg frequency ratio versus the 2:1 ratio observed in non-injured individuals. Shoulder and hip movement patterns, however, are highly reproducible (coordinated) in participants with iSCI, regardless of CWS. This high degree of inter-extremity coordination could reflect an inability to modify a single movement pattern post-iSCI. Combined, these data suggest inter-extremity walking coordination may be altered, but is present after iSCI, and therefore may be regulated, in part, by neural control. Published by Elsevier B.V.},
	number = {1},
	urldate = {2019-07-26},
	journal = {Gait \& Posture},
	author = {Tester, Nicole J and Barbeau, Hugues and Howland, Dena R and Cantrell, Amy and Behrman, Andrea L},
	month = may,
	year = {2012},
	pmid = {22341058},
	pmcid = {PMC3362672},
	pages = {49--55}
}

@article{tester_device_2011,
	title = {Device use, locomotor training and the presence of arm swing during treadmill walking after spinal cord injury.},
	volume = {49},
	url = {http://dx.doi.org/10.1038/sc.2010.128},
	doi = {10.1038/sc.2010.128},
	abstract = {STUDY DESIGN: Observational, cross-sectional study from a convenience sample with pretest/posttest data from a sample subset. OBJECTIVES: Determine the presence of walking-related arm swing after spinal cord injury (SCI), its associated factors and whether arm swing may change after locomotor training (LT). SETTING: Malcom Randall VAMC and University of Florida, Gainesville, FL. METHODS: Arm movement was assessed during treadmill stepping, pre-LT, in 30 individuals with motor incomplete SCI (iSCI, American Spinal Injury Association Impairment Scale grade C/D, as defined by the International Standards for Neurological Classifications of SCI, with neurological level of impairment at or below C4). Partial body weight support and manual-trainer assistance were provided, as needed, to achieve stepping and allow arm swing. Arm swing presence was compared on the basis of cervical versus thoracic neurological levels of impairment and device type. Leg and arm strength and walking independence were compared between individuals with and without arm swing. Arm swing was reevaluated post-LT in the 21 out of 30 individuals who underwent LT. RESULTS: Of 30 individuals with iSCI, 12 demonstrated arm swing during treadmill stepping, pre-LT. Arm movement was associated with device type, lower extremity motor scores and walking independence. Among the 21 individuals who received LT, only 5 demonstrated arm swing pre-LT. Of the 16 individuals lacking arm swing pre-LT, 8 integrated arm swing post-LT. CONCLUSION: Devices routinely used for walking post-iSCI appeared associated with arm swing. Post-LT, arm swing presence increased. Therefore, arm swing may be experience dependent. Daily neuromuscular experiences provided to the arms may produce training effects, thereby altering arm swing expression.},
	number = {3},
	urldate = {2019-07-26},
	journal = {Spinal Cord},
	author = {Tester, N J and Howland, D R and Day, K V and Suter, S P and Cantrell, A and Behrman, A L},
	month = mar,
	year = {2011},
	pmid = {20938449},
	pmcid = {PMC3021654},
	pages = {451--456}
}

@article{masocha_assessment_2009,
	title = {Assessment of weight bearing changes and pharmacological antinociception in mice with {LPS}-induced monoarthritis using the {Catwalk} gait analysis system.},
	volume = {85},
	url = {http://dx.doi.org/10.1016/j.lfs.2009.07.015},
	doi = {10.1016/j.lfs.2009.07.015},
	abstract = {AIMS: We evaluated the possibility of using the video-based Catwalk gait analysis method to measure weight bearing changes and for testing pharmacological antinociception in freely moving mice with lipopolysaccharide (LPS)-induced monoarthritis. MAIN METHODS: LPS or its solvent (PBS) was injected intra-articularly into the right hind (RH) limb ankle joint through the Achilles tendon of C57BL/6 mice. The Catwalk system was used to assess behavioral changes in freely moving mice. The effects of indomethacin on changes in LPS-inoculated mice were examined. KEY FINDINGS: Mice inoculated with LPS into the RH limb showed reduced paw pressure (measured as light intensity) and print area on the RH limb, whereas they exerted more pressure with the left hind (LH) and front limbs, showing a transfer of weight bearing from RH to LH and front limbs, which was significant at 2 days post-LPS inoculation. There were no differences between the front limbs. No changes were observed in the PBS injected controls. There were no changes in interlimb coordination (regularity index) in both PBS- and LPS-injected mice. Treatment with indomethacin (10 and 100mg/kg) restored the weight bearing (measured as the ratio of the pressure exerted by the paws) and the print area ratios of LPS-inoculated mice similar to that observed in control mice. SIGNIFICANCE: This study shows that the Catwalk gait analysis system can be used to objectively quantify LPS-induced monoarthritis weight bearing changes in all four limbs and evaluate pharmacological antinociception in freely moving mice.},
	number = {11-12},
	urldate = {2019-07-26},
	journal = {Life Sciences},
	author = {Masocha, Willias and Parvathy, Subramanian S},
	month = sep,
	year = {2009},
	pmid = {19683012},
	pages = {462--469}
}

@article{lemieux_speed-dependent_2016,
	title = {Speed-{Dependent} {Modulation} of the {Locomotor} {Behavior} in {Adult} {Mice} {Reveals} {Attractor} and {Transitional} {Gaits}.},
	volume = {10},
	url = {http://dx.doi.org/10.3389/fnins.2016.00042},
	doi = {10.3389/fnins.2016.00042},
	abstract = {Locomotion results from an interplay between biomechanical constraints of the muscles attached to the skeleton and the neuronal circuits controlling and coordinating muscle activities. Quadrupeds exhibit a wide range of locomotor gaits. Given our advances in the genetic identification of spinal and supraspinal circuits important to locomotion in the mouse, it is now important to get a better understanding of the full repertoire of gaits in the freely walking mouse. To assess this range, young adult C57BL/6J mice were trained to walk and run on a treadmill at different locomotor speeds. Instead of using the classical paradigm defining gaits according to their footfall pattern, we combined the inter-limb coupling and the duty cycle of the stance phase, thus identifying several types of gaits: lateral walk, trot, out-of-phase walk, rotary gallop, transverse gallop, hop, half-bound, and full-bound. Out-of-phase walk, trot, and full-bound were robust and appeared to function as attractor gaits (i.e., a state to which the network flows and stabilizes) at low, intermediate, and high speeds respectively. In contrast, lateral walk, hop, transverse gallop, rotary gallop, and half-bound were more transient and therefore considered transitional gaits (i.e., a labile state of the network from which it flows to the attractor state). Surprisingly, lateral walk was less frequently observed. Using graph analysis, we demonstrated that transitions between gaits were predictable, not random. In summary, the wild-type mouse exhibits a wider repertoire of locomotor gaits than expected. Future locomotor studies should benefit from this paradigm in assessing transgenic mice or wild-type mice with neurotraumatic injury or neurodegenerative disease affecting gait.},
	urldate = {2019-07-26},
	journal = {Frontiers in Neuroscience},
	author = {Lemieux, Maxime and Josset, Nicolas and Roussel, Marie and Couraud, Sébastien and Bretzner, Frédéric},
	month = feb,
	year = {2016},
	pmid = {26941592},
	pmcid = {PMC4763020},
	pages = {42}
}

@article{aragao_automatic_2011,
	title = {Automatic system for analysis of locomotor activity in rodents–a reproducibility study.},
	volume = {195},
	url = {http://dx.doi.org/10.1016/j.jneumeth.2010.12.016},
	doi = {10.1016/j.jneumeth.2010.12.016},
	abstract = {Automatic analysis of locomotion in studies of behavior and development is of great importance because it eliminates the subjective influence of evaluators on the study. This study aimed to develop and test the reproducibility of a system for automated analysis of locomotor activity in rats. For this study, 15 male Wistar were evaluated at P8, P14, P17, P21, P30 and P60. A monitoring system was developed that consisted of an open field of 1m in diameter with a black surface, an infrared digital camera and a video capture card. The animals were filmed for 2 min as they moved freely in the field. The images were sent to a computer connected to the camera. Afterwards, the videos were analyzed using software developed using MATLAB® (mathematical software). The software was able to recognize the pixels constituting the image and extract the following parameters: distance traveled, average speed, average potency, time immobile, number of stops, time spent in different areas of the field and time immobile/number of stops. All data were exported for further analysis. The system was able to effectively extract the desired parameters. Thus, it was possible to observe developmental changes in the patterns of movement of the animals. We also discuss similarities and differences between this system and previously described systems. {\textbackslash}copyright 2010 Elsevier B.V. All rights reserved.},
	number = {2},
	urldate = {2019-07-26},
	journal = {Journal of Neuroscience Methods},
	author = {Aragão, Raquel da Silva and Rodrigues, Marco Aurélio Benedetti and de Barros, Karla Mônica Ferraz Teixeira and Silva, Sebastião Rogério Freitas and Toscano, Ana Elisa and de Souza, Ricardo Emmanuel and Manhães-de-Castro, Raul},
	month = feb,
	year = {2011},
	pmid = {21182870},
	pages = {216--221}
}

@article{park_method_2014,
	title = {A method for generating a mouse model of stroke: evaluation of parameters for blood flow, behavior, and survival [corrected].},
	volume = {23},
	url = {http://dx.doi.org/10.5607/en.2014.23.1.104},
	doi = {10.5607/en.2014.23.1.104},
	abstract = {Stroke is one of the common causes of death and disability. Despite extensive efforts in stroke research, therapeutic options for improving the functional recovery remain limited in clinical practice. Experimental stroke models using genetically modified mice could aid in unraveling the complex pathophysiology triggered by ischemic brain injury. Here, we optimized the procedure for generating mouse stroke model using an intraluminal suture in the middle cerebral artery and verified the blockage of blood flow using indocyanine green coupled with near infra-red radiation. The first week after the ischemic injury was critical for survivability. The survival rate of 11\% in mice without any treatment but increased to 60\% on administering prophylactic antibiotics. During this period, mice showed severe functional impairment but recovered spontaneously starting from the second week onward. Among the various behavioral tests, the pole tests and neurological severity score tests remained reliable up to 4 weeks after ischemia, whereas the rotarod and corner tests became less sensitive for assessing the severity of ischemic injury with time. Further, loss of body weight was also observed for up 4 weeks after ischemia induction. In conclusion, we have developed an improved approach which allows us to investigate the role of the cell death-related genes in the disease progression using genetically modified mice and to evaluate the modes of action of candidate drugs.},
	number = {1},
	urldate = {2019-07-26},
	journal = {Experimental neurobiology},
	author = {Park, Sin-Young and Marasini, Subash and Kim, Geu-Hee and Ku, Taeyun and Choi, Chulhee and Park, Min-Young and Kim, Eun-Hee and Lee, Young-Don and Suh-Kim, Haeyoung and Kim, Sung-Soo},
	month = mar,
	year = {2014},
	pmid = {24737945},
	pmcid = {PMC3984953},
	pages = {104--114}
}

@article{bailoo_precision_2010,
	title = {The precision of video and photocell tracking systems and the elimination of tracking errors with infrared backlighting.},
	volume = {188},
	url = {http://dx.doi.org/10.1016/j.jneumeth.2010.01.035},
	doi = {10.1016/j.jneumeth.2010.01.035},
	abstract = {Automated tracking offers a number of advantages over both manual and photocell tracking methodologies, including increased reliability, validity, and flexibility of application. Despite the advantages that video offers, our experience has been that video systems cannot track a mouse consistently when its coat color is in low contrast with the background. Furthermore, the local lab lighting can influence how well results are quantified. To test the effect of lighting, we built devices that provide a known path length for any given trial duration, at a velocity close to the average speed of a mouse in the open-field and the circular water maze. We found that the validity of results from two commercial video tracking systems (ANY-maze and EthoVision XT) depends greatly on the level of contrast and the quality of the lighting. A photocell detection system was immune to lighting problems but yielded a path length that deviated from the true length. Excellent precision was achieved consistently, however, with video tracking using infrared backlighting in both the open field and water maze. A high correlation (r=0.98) between the two software systems was observed when infrared backlighting was used with live mice. Copyright 2010 Elsevier B.V. All rights reserved.},
	number = {1},
	urldate = {2019-07-26},
	journal = {Journal of Neuroscience Methods},
	author = {Bailoo, Jeremy D and Bohlen, Martin O and Wahlsten, Douglas},
	month = apr,
	year = {2010},
	pmid = {20138914},
	pmcid = {PMC2847046},
	pages = {45--52}
}

@article{samson_mousemove:_2015,
	title = {{MouseMove}: an open source program for semi-automated analysis of movement and cognitive testing in rodents.},
	volume = {5},
	url = {http://dx.doi.org/10.1038/srep16171},
	doi = {10.1038/srep16171},
	abstract = {The Open Field (OF) test is one of the most commonly used assays for assessing exploratory behaviour and generalised locomotor activity in rodents. Nevertheless, the vast majority of researchers still rely upon costly commercial systems for recording and analysing OF test results. Consequently, our aim was to design a freely available program for analysing the OF test and to provide an accompanying protocol that was minimally invasive, rapid, unbiased, without the need for specialised equipment or training. Similar to commercial systems, we show that our software-called MouseMove-accurately quantifies numerous parameters of movement including travel distance, speed, turning and curvature. To assess its utility, we used MouseMove to quantify unilateral locomotor deficits in mice following the filament-induced middle cerebral artery occlusion model of acute ischemic stroke. MouseMove can also monitor movement within defined regions-of-interest and is therefore suitable for analysing the Novel Object Recognition test and other field-related cognitive tests. To the best of our knowledge, MouseMove is the first open source software capable of providing qualitative and quantitative information on mouse locomotion in a semi-automated and high-throughput fashion, and hence MouseMove represents a sound alternative to commercial movement analysis systems.},
	urldate = {2017-04-10},
	journal = {Scientific reports},
	author = {Samson, Andre L and Ju, Lining and Ah Kim, Hyun and Zhang, Shenpeng R and Lee, Jessica A A and Sturgeon, Sharelle A and Sobey, Christopher G and Jackson, Shaun P and Schoenwaelder, Simone M},
	month = nov,
	year = {2015},
	pmid = {26530459},
	pmcid = {PMC4632026},
	pages = {16171}
}

@book{bishop_pattern_2006,
	address = {New York},
	series = {Information {Science} and {Statistics}},
	title = {Pattern {Recognition} and {Machine} {Learning}},
	isbn = {978-0-387-31073-2},
	url = {https://www.springer.com/de/book/9780387310732},
	abstract = {The dramatic growth in practical applications for machine learning over the last ten years has been accompanied by many important developments in the underlying algorithms and techniques. For example, Bayesian methods have grown from a specialist niche to become mainstream, while graphical models have emerged as a general framework for describing and applying probabilistic techniques. The practical applicability of Bayesian methods has been greatly enhanced by the development of a range of approximate inference algorithms such as variational Bayes and expectation propagation, while new models based on kernels have had a significant impact on both algorithms and applications. This completely new textbook reflects these recent developments while providing a comprehensive introduction to the fields of pattern recognition and machine learning. It is aimed at advanced undergraduates or first-year PhD students, as well as researchers and practitioners. No previous knowledge of pattern recognition or machine learning concepts is assumed. Familiarity with multivariate calculus and basic linear algebra is required, and some experience in the use of probabilities would be helpful though not essential as the book includes a self-contained introduction to basic probability theory. The book is suitable for courses on machine learning, statistics, computer science, signal processing, computer vision, data mining, and bioinformatics. Extensive support is provided for course instructors, including more than 400 exercises, graded according to difficulty. Example solutions for a subset of the exercises are available from the book web site, while solutions for the remainder can be obtained by instructors from the publisher. The book is supported by a great deal of additional material, and the reader is encouraged to visit the book web site for the latest information. Christopher M. Bishop is Deputy Director of Microsoft Research Cambridge, and holds a Chair in Computer Science at the University of Edinburgh. He is a Fellow of Darwin College Cambridge, a Fellow of the Royal Academy of Engineering, and a Fellow of the Royal Society of Edinburgh. His previous textbook "Neural Networks for Pattern Recognition" has been widely adopted. Coming soon: *For students, worked solutions to a subset of exercises available on a public web site (for exercises marked "www" in the text) *For instructors, worked solutions to remaining exercises from the Springer web site *Lecture slides to accompany each chapter *Data sets available for download},
	language = {en},
	urldate = {2020-06-28},
	publisher = {Springer-Verlag},
	author = {Bishop, Christopher},
	year = {2006},
}

@misc{bosch_engineering_2021,
	type = {chapter},
	title = {Engineering {AI} {Systems}: {A} {Research} {Agenda}},
	copyright = {Access limited to members},
	shorttitle = {Engineering {AI} {Systems}},
	url = {www.igi-global.com/chapter/engineering-ai-systems/266130},
	abstract = {Artificial intelligence (AI) and machine learning (ML) are increasingly broadly adopted in industry. However, based on well over a dozen case studies, we have learned that deploying industry-strength, production quality ML models in systems proves to be challenging. Companies experience challenges r...},
	language = {en},
	urldate = {2021-02-02},
	journal = {Artificial Intelligence Paradigms for Smart Cyber-Physical Systems},
	author = {Bosch, Jan and Olsson, Helena Holmström and Crnkovic, Ivica},
	year = {2021},
	doi = {10.4018/978-1-7998-5101-1.ch001},
	note = {ISBN: 9781799851011
Pages: 1-19
Publisher: IGI Global},
}

@article{shenk_automated_2020,
	title = {Automated {Analysis} of {Stroke} {Mouse} {Trajectory} {Data} {With} {Traja}},
	volume = {14},
	issn = {1662-453X},
	url = {https://www.frontiersin.org/articles/10.3389/fnins.2020.00518/full},
	doi = {10.3389/fnins.2020.00518},
	abstract = {Quantitative characterization of mouse activity, locomotion and walking patterns requires the monitoring of position and activity over long periods of time. Manual behavioral phenotyping, however, is time and skill-intensive, vulnerable to researcher bias and often stressful for the animals. We present examples for using a platform-independent open source trajectory analysis software, Traja, for semi-automated analysis of high throughput mouse home-cage data for neurobehavioral research. Our software quantifies numerous parameters of movement including travelled distance, velocity, turnings, and laterality which are demonstrated for application to neurobehavioral analysis. In this study, the open source software for trajectory analysis Traja is applied to movement and walking pattern observations of transient stroke induced female C57BL/6 mice (30 min middle cerebral artery occlusion) on an acute multinutrient diet intervention (Fortasyn). Mice were housed individually in Digital Ventilated Cages (DVC, GM500, Tecniplast S.p.A., Buguggiate (VA), Italy) and activity was recorded 24/7, every 250 ms using a DVC board. Significant changes in activity, velocity, and distance walked are computed with Traja. Traja identified increased walked distance and velocity in Control and Fortasyn animals over time. No diet effect was found in preference of turning direction (laterality) and distance travelled. As open source software for trajectory analysis, Traja supports independent development and validation of numerical methods and provides a useful tool for computational analysis of 24/7 mouse locomotion in home-cage environment for application in behavioral research or movement disorders.},
	language = {English},
	urldate = {2020-12-21},
	journal = {Frontiers in Neuroscience},
	author = {Shenk, Justin and Lohkamp, Klara J. and Wiesmann, Maximilian and Kiliaan, Amanda J.},
	year = {2020},
	note = {Publisher: Frontiers},
	keywords = {animal tracking, Home-cage, machine learning, Mouse, neuropsychiatric disorders, Stroke},
	file = {Full Text PDF:C\:\\Users\\hpaye\\Zotero\\storage\\IBNLUH9P\\Shenk et al. - 2020 - Automated Analysis of Stroke Mouse Trajectory Data.pdf:application/pdf},
}

@misc{shenk_towards_2020,
	title = {Towards {Explainable} {AI} with {Feature} {Space} {Exploration}},
	url = {https://towardsdatascience.com/towards-explainable-ai-with-feature-space-exploration-628930baf8ef},
	abstract = {Neural networks trained on large amounts of data have led to incredible technological leaps affecting nearly every part of our lives.},
	language = {en},
	urldate = {2021-02-08},
	journal = {Medium},
	author = {Shenk, Justin},
	month = jun,
	year = {2020},
}

@book{grus_data_2015,
	address = {Beijing},
	title = {Data {Science} from {Scratch}: {First} {Principles} with {Python}},
	isbn = {978-1-4919-0142-7},
	url = {http://my.safaribooksonline.com/97814919-01427},
	abstract = {Data science libraries, frameworks, modules, and toolkits are great for doing data science, but they're also a good way to dive into the discipline without actually understanding data science. In this book, you'll learn how many of the most fundamental data science tools and algorithms work by implementing them from scratch. If you have an aptitude for mathematics and some programming skills, author Joel Grus will help you get comfortable with the math and statistics at the core of data science, and with hacking skills you need to get started as a data scientist.},
	publisher = {O'Reilly},
	author = {Grus, Joel},
	year = {2015},
	keywords = {01624 103 safari book ai software development data pattern recognition analysis python},
}

@article{chandra_traphic_2019,
	title = {{TraPHic}: {Trajectory} {Prediction} in {Dense} and {Heterogeneous} {Traffic} {Using} {Weighted} {Interactions}},
	url = {http://arxiv.org/abs/1812.04767 https://arxiv.org/abs/1812.04767},
	journal = {arXiv:1812.04767 [cs]},
	author = {Chandra, Rohan and Bhattacharya, Uttaran and Bera, Aniket and Manocha, Dinesh},
	year = {2019},
	doi = {10.1109/cvpr.2019.00868},
	note = {Type: Journal Article},
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib