Robust, Rapid, and Accurate Detection of Mice in Video Using Convolutional and Recurrent Neural Networks

In the field of neuroscience, in vivo animal studies are a common form of basic research. Within those studies, and prior to ex vivo analysis of tissue samples, there is almost always a need to record and analyze the activity of the subjects. As techniques to image cause and effect on a synaptic level improve and strides are being made to model and synthesize neurological conditions, a smaller portion of neuroscience literature makes behavior analysis a priority. Despite these advances, behavioral analysis is often instrumental in understanding how the specific changes to the brain have an effect on the underlying systems of the test subjects. Neuroscience often relied on estimations of activity from manual monitoring or physical mechanisms (e.g. beam breaking), but there are limitations to these collection methods. For example, human monitoring of activity is prone to error and cannot be maintained across long periods of time. While physical monitoring often does not capture the full richness of behavior, reporting data in the form of "activity counts" or "beam breaks". In order to automate and improve the quality of detection, computational methods of capturing behavior and activity were developed. Using multiple traditional computer vision techniques, some for-profit companies have created monitoring solutions at great cost to institutions. However, there are limitations to these systems in that they are brittle, e.g. susceptible to errors when changing the environment or video recording quality. While there has been some public research using more traditional machine learning algorithms to track activity and behavior, the newer machine learning algorithms appear mostly in patents. In this work, a couple of well-known, modern object detection models (YOLOv3 and RetinaNet) are tested, with and without modifications, to introduce the viability of these mechanisms to track activity of multiple strains of mice during high activity states (e.g. hanging, jumping, walking, and rearing). Additionally, to facilitate development of training data for modern neural networks, a collaborative annotation framework was created and hosted (available at https://ourlabels.org). This work determines that a robust, faster than real-time, and accurate system can be developed to tally activity during high activity states while relying on very little training data, transfer learning, and minimal modification to the object detection system.An analysis of methods to produce real time, accurate behavior phenotyping of mice using RetinaNet and modified YOLOv3 with recurrent neural networks

Evaluation of the multispecimen parallel differential pTRM method: a test on historical lavas from Iceland and Mexico

Accepted versio

Long-lived magnetism on chondrite parent bodies

publisher: Elsevier articletitle: Long-lived magnetism on chondrite parent bodies journaltitle: Earth and Planetary Science Letters articlelink: http://dx.doi.org/10.1016/j.epsl.2017.07.035 content_type: article copyright: © 2017 The Authors. Published by Elsevier B.V.© 2017 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). The attached file is the published version of the article

A comparison of Thellier-type and multispecimen paleointensity determinations on Pleistocene and historical lava flows from Lanzarote (Canary Islands, Spain)

Sixteen Miocene, Pleistocene, and historic lava flows have been sampled in Lanzarote (Canary Islands) for paleointensity analysis with both the Coe and multispecimen methods. Besides obtaining new data, the main goal of the study was the comparison of paleointensity results determined with two different techniques. Characteristic Remanent Magnetization (ChRM) directions were obtained in 15 flows, and 12 were chosen for paleointensity determination. In Thellier-type experiments, a selection of reliable paleointensity determinations (43 of 78 studied samples) was performed using sets of criteria of different stringency, trying to relate the quality of results to the strictness of the chosen criteria. Uncorrected and fraction and domain-state corrected multispecimen paleointensity results were obtained in all flows. Results with the Coe method on historical flows either agree with the expected values or show moderately lower ones, but multispecimen determinations display a large deviation from the expected result in one case. No relation can be detected between correct or anomalous results and paleointensity determination quality or rock-magnetic properties. However, results on historical flows suggest that agreement between both methods could be a good indicator of correct determinations. Comparison of results obtained with both methods on seven Pleistocene flows yields an excellent agreement in four and disagreements in three cases. Pleistocene determinations were only accepted if either results from both methods agreed or a result was based on a sufficiently large number (n>4) of individual Thellier-type determinations. In most Pleistocene flows, a VADM around 5 31022 Am2 was observed, although two flows displayed higher values around 931022 Am2.project CGL2012-32149 (Ministerio de Econom ıa y Competitividad, Spain), project 320/2011 (Ministerio de Medio Ambiente y Medio Rural y Marino, Spain) and the European Regional Development Fund (ERDF)

Paleointensity Record From the 2.7 Ga Stillwater Complex, Montana

The record of geomagnetic intensity captured in the 2.7 Ga Stillwater Complex (Montana, USA) provides a statistical description of the Archean geodynamo. We present results of modified Thellier paleointensity experiments on 441 core specimens, 114 of which pass strict reliability criteria. The specimens are from 53 sites spanning most of the Banded Series rocks in the Stillwater Complex. On the basis of thermochronologic and petrologic evidence, we interpret the highest temperature component of remanence to be a late Archean thermoremanence, though the possibility remains that it is a thermochemical remanence. Thermal models indicate that the highest temperature magnetization component at each of the sites averages ∼20–200 ka of geomagnetic secular variation. The suite of sites as distributed through the Banded Series samples a roughly a 1 Ma time interval. The average of the most reliable paleointensity measurements, uncorrected for the effects of anisotropy or cooling rate, is 38.2 ± 11.3 μT (1σ). Remanence anisotropy, cooling rate, and the nonlinear relationship between applied field and thermoremanence have a significant effect on paleointensity results; a corrected average of 30.6 ± 8.8 μT is likely a more appropriate value. Earth\u27s average dipole moment during the late Archean (5.05 ± 1.46 × 1022Am2, λpmag = 44.5°) was well within the range of estimates from Phanerozoic rocks. The distribution of site-mean paleointensities around the mean is consistent with that expected from slow cooling over timescales expected from thermal models and with secular variation comparable to that of the Phanerozoic field

Source of oceanic magnetic anomalies and the geomagnetic polarity time scale

Marine magnetic anomalies provide the framework for the geomagnetic polarity timescale for the Late Jurassic to Recent (since 160 Ma). Magnetostratigraphic records confirm that the polarity reversal sequence interpreted from magnetic anomalies is complete to a resolution of better than 30 ky. In addition to this record of polarity reversals, magnetic anomalies also appear to preserve information on geomagnetic intensity fluctuations. The correspondence of coherent near-bottom anomaly variations with independent estimates of field intensity provides strong evidence that geomagnetic intensity modulates the magnetization of the ocean crust. Indeed, many short wavelength anomaly variations in sea-surface magnetic profiles over fast-spreading ridges are likely attributable to geomagnetic intensity variations. Although longer-term geomagnetic field behavior may also be reflected in anomaly amplitudes, documenting such a signal requires a better understanding of time-dependent changes in the magnetic source (e.g., from low-temperature alteration) that may also affect magnetic anomalies. The extrusive layer, with an average remanence of ∼ 5 A m−1, is the largest contributor to magnetic anomalies. However, enhanced sampling of oceanic gabbros (average remanence ∼ 1 A m−1) and, to a lesser extent, dikes (average remanence ∼ 2 A m−1) reveals that these deeper (and thicker) layers likely generate anomalies comparable to those from the lavas. Lava accumulation at intermediate- and fast-spreading ridges typically occurs over a narrow (1–3 km) region and dike emplacement is even more narrowly confined, resulting in a relatively high fidelity record of geomagnetic field behavior. The slow cooling of the gabbroic layer, however, results in gently dipping polarity boundaries that significantly affect the skewness of the resulting anomalies, which is also a sensitive measure of net rotations of the source layer(s). The magnetizations of the dikes and gabbros are characterized by high stability and are not expected to significantly change with time, although there are insufficient data to confirm this. The lavas, however, typically show evidence of low-temperature alteration, which has been long regarded as a process that progressively reduces the magnetization (and degrades the geomagnetic signal) in the extrusive layer and reduces the amplitude of magnetic anomalies. Sufficient data have become available to examine this conventional wisdom. There is a substantial (∼ 4x) reduction in magnetization from on-axis samples to immediately off-axis drillsites (∼ 0.5 My), but little further change in half-dozen or so deep crustal sites to ∼ 160 Ma. High paleointensity that characterizes the last few thousand years may contribute significantly to the high on-axis magnetization. The task of evaluating changes in remanence of the extrusive layer is made more difficult by substantial cooling-rate-dependent changes in magnetic properties and the systematic variation in remanence with iron content (magnetic telechemistry). The commonly cited magnetic anomaly amplitude envelope is in fact not systematically observed – the Central Anomaly is elevated at slow-spreading ridges but is not as prominent at faster spreading rates. Nonetheless, magnetic anomaly amplitudes are consistent with magnetization change is poorly constrained. Direct determinations of the degree of low-temperature oxidation reveal the presence of highly oxidized titanomagnetite in samples less than 1 My old, suggesting a short (∼ 105 years) time constant though the effects of low-temperature oxidation are quite heterogeneous. While low-temperature oxidation does have some affect on lava magnetization and anomaly amplitudes, there is increasing evidence that marine magnetic anomalies are capable of recording a broad spectrum of geomagnetic field behavior, ranging from millennial-scale paleointensity variations to polarity reversals to apparent polar wander to, more speculatively, long-term changes in average field strength. Several emerging tools and approaches – autonomous vehicles, oriented samples, absolute paleointensity of near-ridge lavas, and measurements of the vector anomalous field – are therefore likely to significantly advance our understanding of the geomagnetic signal recorded in the oceanic crust, as well as our ability to utilize this information in addressing outstanding problems in crustal accretion processes

Paleomagnetic Results from the Snake River Plain: Contribution to the Time-Averaged Field Global Database

This study presents paleomagnetic results from the Snake River Plain (SRP) in southern Idaho as a contribution to the time-averaged field global database. Paleomagnetic samples were measured from 26 sites, 23 of which ( 13 normal, 10 reverse) yielded site mean directions meeting our criteria for acceptable paleomagnetic data. Flow ages (on 21 sites) range from 5 ka to 5.6 Ma on the basis of Ar-40/Ar-39 dating methods. The age and polarity for the 21 dated sites are consistent with the Geomagnetic Reversal Time Scale except for a single reversely magnetized site dated at 0.39 Ma. This is apparently the first documented excursion associated with a period of low paleointensity detected in both sedimentary and igneous records. Combining the new data from the SRP with data published from the northwest United States between the latitudes of 40degrees and 50degreesN, there are 183 sites in all that meet minimum acceptability criteria for legacy and new data. The overall mean direction of 173 normally magnetized sites has a declination of 2.3degrees, inclination of 61.4degrees, a Fisher concentration parameter (kappa) of 58, and a radius of 95% confidence (alpha(95)) of 1.4degrees. Reverse sites have a mean direction of 182.4degrees declination, -58.6degrees inclination, kappa of 50, and alpha(95) of 6.9degrees. Normal and reversed mean directions are antipodal and indistinguishable from a geocentric axial dipole field at the 95% confidence level. Virtual geomagnetic pole dispersion was found to be circularly symmetric, while the directional data were elongate north-south. An updated and corrected database for the northwestern U. S. region has been contributed to the Magnetics Information Consortium (MagIC) database at http://earthref.org