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- Creator:
- Vaskov, Alex K, Vu, Philip P, North, Naia, Davis, Alicia J, Kung, Theodore A, Gates, Deanna H, Cederna, Paul S, and Chestek, Cynthia A
- Description:
- The data was used to calibrate and simulate pattern recognition algorithms for the following publication: Surgically Implanted Electrodes Enable Real-Time Finger and Grasp Pattern Recognition for Prosthetic Hands (medRxiv 2020, IEEE TRO in review). Each data file is named as follows Px_PostureSet.csv. Where Px is the patient number. The 1 of 10 posture set contains individual finger and intrinsic thumb movements, the grasps posture set contains a fewer number of combined finger movements. P1’s calibration data for individual fingers is labelled 1 of 12 because it also includes two grasps, which were removed for analysis in the publication. The first column of each .csv file is the experiment time in seconds. The second column is the posture of the cue hand at that timestamp. The rest of the columns are the raw EMG data in microvolts sampled at 30KSps. A legend of the movement postures, each patients EMG channels, and suggested signal processing and filtering is included in DataLabellingAndProcessing.pdf
- Keyword:
- pattern recognition, electromyography, regenerative peripheral nerve interface, intramuscular electrodes, and myoelectric prostheses
- Citation to related publication:
- Surgically Implanted Electrodes Enable Real-Time Finger and Grasp Pattern Recognition for Prosthetic Hands A. K. Vaskov, P. P. Vu, N. North, A. J. Davis, T. A. Kung, D. H. Gates, P. S. Cederna, C. A. Chestek medRxiv 2020.10.28.20217273; doi: https://doi.org/10.1101/2020.10.28.20217273
- Discipline:
- Science and Engineering
-
- Creator:
- Ding, J, Moore, TY, and Gan, Z
- Description:
- Jerboas (Jaculus jaculus) are bipedal hopping rodents that frequently transition between gaits (running, hopping, and skipping) throughout their entire speed range. It has been hypothesized that these non-cursorial bipedal gait transitions are likely to enhance their maneuverability and predator evasion ability. However, it is difficult to use the underlying dynamics of these locomotion patterns to predict gait transitions due to the large number of degrees of freedom expressed by the animals. To this end, we used empirical jerboa kinematics and dynamics to develop a unified Spring Loaded Inverted Pendulum model with defined passive swing leg motions. The simulated trajectories from the model precisely matched the experimental data. Jerboas were observed to apply different neutral swing leg angles during locomotion. By investigating the gait structure of the model with coupled and uncoupled neutral swing leg, we found two set of mechanism may explain the frequent gait transitions of jerboas.
- Keyword:
- jerboa, legged locomotion, gait transition, Legged Robots, Dynamics, Bipedal locomotion, and Non-cursorial locomotion
- Citation to related publication:
- Ding, Moore, Gan (submitted) A template model explains jerboa gait transitions across a broad range of speeds. Frontiers in Bioengineering And Biotechnology
- Discipline:
- Science and Engineering
-
- Creator:
- BIRDS Lab, U. Michigan
- Description:
- These data were produced for ARO W911NF-14-1-0573 "Morphologically Modulated Dynamics" and ARO MURI W911NF-17-1-0306 "From Data-Driven Operator Theoretic Schemes to Prediction, Inference, and Control of Systems" to explore the trade-offs between various oscillator coupling models in modeling multilegged locomotion of Multipod robots with 6,8,10 and 12 legs. The data is stored in .csv.gz files, one file for each robot morphology. Details of how to run the processing code on the raw dataset to generate the processed files found here, as well as example code for loading the data found here, are in the README. This dataset is self contained and can be used on its own without running any of the provided code.
- Citation to related publication:
- Zhao, D. & Revzen, S. Multi-legged steering and slipping with low DoF hexapod robots Bioinspiration & biomimetics, 2020, 15, 045001 https://doi.org/10.1088/1748-3190/ab84c0, Zhao, D. Ph.D. Thesis "Locomotion of low-DOF multi-legged robots" University of Michigan 2021 https://deepblue.lib.umich.edu/handle/2027.42/169985, and BIRDS Lab Multipod robot motion tracking data - RAW data, doi:10.7302/m05a-0d90
- Discipline:
- Engineering and Science
-
- Creator:
- Curlis, JD, Renney, TJ, Davis Rabosky, AR, and Moore, TY
- Description:
- Efficient comparisons of biological color patterns are critical for understanding the mechanisms by which organisms evolve in ecosystems, including sexual selection, predator-prey interactions, and thermoregulation. However, elongate or spiral-shaped organisms do not conform to the standard orientation and photographic techniques required for automated analysis. Currently, large-scale color analysis of elongate animals requires time-consuming manual landmarking, which reduces their representation in coloration research despite their ecological importance. We present Batch-Mask: an automated and customizable workflow to facilitate the analysis of large photographic data sets of non-standard biological subjects. First, we present a user guide to run an open-source region-based convolutional neural network with fine-tuned weights for identifying and isolating a biological subject from a background (masking). Then, we demonstrate how to combine masking with existing manual visual analysis tools into a single streamlined, automated workflow for comparing color patterns across images. Batch-Mask was 60x faster than manual landmarking, produced masks that correctly identified 96% of all snake pixels, and produced pattern energy results that were not significantly different from the manually landmarked data set. The fine-tuned weights for the masking neural network, user guide, and automated workflow substantially decrease the amount of time and attention required to quantitatively analyze non-standard biological subjects. By using these tools, biologists will be able to compare color, pattern, and shape differences in large data sets that include significant morphological variation in elongate body forms. This advance will be especially valuable for comparative analyses of natural history collections, and through automation can greatly expand the scale of space, time, or taxonomic breadth across which color variation can be quantitatively examined.
- Keyword:
- convolutional neural network, photography, sensory ecology, color evolution, vision, and image segmentation
- Citation to related publication:
- Curlis, Renney, Davis Rabosky, Moore (submitted) Batch-Mask: An automated Mask R-CNN workflow to isolate non-standard biological specimens for color pattern analysis.
- Discipline:
- Engineering and Science
-
- Creator:
- Moore, Talia Y, Villacis Nunez, C Nathaly, Ray, Andrew P, and Cooper, Kimberly L
- Description:
- Hind limbs can undergo dramatic changes in loading conditions during the transition from quadrupedal to bipedal locomotion. For example, the most early diverging bipedal jerboas (Rodentia: Dipodidae) are some of the smallest mammals in the world, with body masses that range 2-4 grams. The larger jerboa species exhibit developmental and evolutionary fusion of the central three metatarsals into a single cannon bone. We hypothesize that body size reduction and metatarsal fusion are mechanisms to maintain the safety factor of the hind limb bones despite the higher ground reaction forces associated with bipedal locomotion. Using finite element analysis to model collisions between the substrate and the metatarsals, we found that body size reduction was insufficient to reduce bone stress on unfused metatarsals, based on the scaled dynamics of larger jerboas, and that fused bones developed lower stresses than unfused bones when all metatarsals are scaled to the same size and loading conditions. Based on these results, we conclude that fusion reinforces larger jerboa metatarsals against high ground reaction forces. Because smaller jerboas with unfused metatarsals develop higher peak stresses in response to loading conditions scaled from larger jerboas, we hypothesize that smaller jerboas use alternative dynamics of bipedal locomotion that reduces the impact of collisions between the foot and substrate.
- Keyword:
- finite element, functional morphology, bipedal, jerboa, metatarsus, and bone fusion
- Citation to related publication:
- Villacis Nunez, Ray, Cooper, Moore (submitted). Body size reduction and metatarsal fusion were distinct mechanisms to resist bending as jerboas (Dipodidae) transitioned from quadrupedal to bipedal.
- Discipline:
- Science and Engineering
-
- Creator:
- Brandt, Daniel, A. and Ridley, Aaron, J.
- Description:
- The research that produced this data focused on conducting a statistical comparison between horizontal winds modeled with GITM and those derived from the accelerometer aboard the GOCE satellite. The winds from GITM and GOCE were compared by constructing their respective probability densities under different levels of geomagnetic activity, and by distributing them as a function of geomagnetic activity, magnetic latitude, magnetic local time, day-of-the-year, and solar radio flux.
- Keyword:
- Thermosphere, GITM, GOCE, Neutral winds, and Thermospheric modeling
- Discipline:
- Science and Engineering
-
- Creator:
- Wu, Ziyou, Brunton, Steven L, and Revzen, Shai
- Description:
- These codes were produced as part of the Army Research Office Multi-University Research Initiative ARO MURI W911NF-17-1-0306 "From Data-Driven Operator Theoretic Schemes to Prediction, Inference, and Control of Systems" The code can be run using the runAll.sh shell script (in Linux and OS-X); code should work similarly under windows.
- Keyword:
- DMD, dimensionality reduction, dynamical systems, and nonlinear dynamics
- Discipline:
- Engineering and Science
-
- Creator:
- Revzen, Shai
- Description:
- This repository contains both the data and python3 code that reads this data and reproduces the relevant figures. The code depends on NumPy >1.17 and matplotlib >3.1 and was tested on python 3.8
- Keyword:
- locomotion, slipping, low Reynolds number, walking, and slithering
- Discipline:
- Science and Engineering
-
- Creator:
- BIRDS Lab, U. Michigan
- Description:
- These data were produced in an attempt to characterize the turning and steering behaviors of 1-DoF multi-legged (hexpedal in this case) robots. Such turning behaviors require sliding contact points. All the data is provided in a single, large .csv.gz file (416256 rows); additional details and example code in the README
- Keyword:
- robot, multilegged, and steering
- Citation to related publication:
- BIRDS Lab, U. BigAnt v6 robot motion tracking data - RAW dataset [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/024q-kk06, Revzen, S., & Guckenheimer, J. (2008). Estimating the phase of synchronized oscillators. Phys. Rev. E, 78, 051907. http://dx.doi.org/10.1103/PhysRevE.78.051907, and Dan Zhao and Shai Revzen 2020 Bioinspir. Biomim. 15 045001 https://doi.org/10.1088/1748-3190/ab84c0
- Discipline:
- Engineering
-
- Creator:
- BIRDS Lab, U. Michigan
- Description:
- These data were produced in an attempt to characterize the turning and steering behaviors of 1-DoF multi-legged (hexpedal in this case) robots. Such turning behaviors require sliding contact points. The .tar file contains multiple trials in .csv.gz format, with names following an informative naming convention documented in the README. Additional metadata for the trials is given in the metadata.py file in both machine and human readable form.
- Keyword:
- robot, multilegged, and steering
- Citation to related publication:
- Dan Zhao and Shai Revzen 2020 Bioinspir. Biomim. 15 045001 https://doi.org/10.1088/1748-3190/ab84c0
- Discipline:
- Engineering
-
- Creator:
- Bougher, S. W. (CLaSP Department, University of Michigan)
- Description:
- The NASA MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft, which is currently in orbit around Mars, has been taking systematic measurements of the densities and deriving temperatures in the upper atmosphere of Mars between about 140 to 240 km above the surface since late 2014. Wind measurement campaigns are also conducted once per month for 5-10 orbits. These densities, temperatures and winds change with time (e.g. solar cycle, season, local time) and location, and sometimes fluctuate quickly. Global dust storm events are also known to significantly impact these density, temperature and wind fields in the Mars thermosphere. For the current project, the inert light species helium is used to trace the circulation patterns and constrain wind magnitudes throughout the Mars thermosphere. Presently, more than 6 years of Neutral Gas and Ion Mass Spectrometer (NGIMS) measurements of helium densities have been obtained by the MAVEN team (e.g. Elrod et al., 2017; 2021; Gupta et al., 2021). Measured helium distributions are compared to simulations from a computer model of the Mars atmosphere called M-GITM (Mars Global Ionosphere-Thermosphere Model), developed at U. of Michigan. Since the global circulation plays a role in the structure, variability, and evolution of the atmosphere, understanding the processes that drive the winds in the upper atmosphere of Mars also provides the needed context for understanding helium distributions and how the atmosphere behaves as a whole system. Three dimensional M-GITM simulations for the Mars four cardinal seasons (Ls = 0, 90, 180, 270, for Mars Year 33) were conducted for detailed comparisons with NGIMS helium and CO2 distributions (Gupta et al. 2021). The M-GITM datacubes used to extract these densities (plus winds) along the trajectory of each orbit path between 140 and 240 km, are provided in this Deep Blue Data archive. README files are also provided for each datacube, detailing the contents of each file. In addition, a general README file is provided that summarizes the inputs and outputs of the M-GITM code simulations for this study. Finally, a basic version of the M-GITM code can be found on Github at https:/github.com/dpawlows/MGITM.
- Keyword:
- Mars, MAVEN Spacecraft Mission, Mars Thermosphere, Helium Density Distributions, and Neutral Gas and Ion Mass Spectrometer (NGIMS)
- Citation to related publication:
- Gupta, N., N. V. Rao, S. W. Bougher, and M. K. Elrod, Latitudinal and Seasonal Asymmetries of the Helium Bulge in the Martian Upper Atmosphere J. Geophys. Res., 126, XXXX-XXXX. doi:10.1002/2021JEXXXXXX
- Discipline:
- Engineering and Science
-
- Creator:
- Nason, Samuel R., Mender, Matthew J., Vaskov, Alex K., Willsey, Matthew S., Ganesh Kumar, N., Kung, Theodore A., Patil, Parag G., and Chestek, Cynthia A.
- Description:
- This data is a subset of the data used to generate components of all figures in the manuscript and supplement in Nason et al., 2021, Neuron. The purpose of the study was to demonstrate the first-ever simultaneous brain-control of two independent groups of fingers in one hand with some analysis of cortical tuning to finger movements in nonhuman primates. This advises future brain-machine interfaces for the control of finger movements with humans. All of the data is contained in .mat files, which can be commonly opened by Matlab and the Python scipy library. The Matlab packages (and versions) used for the manuscript are: MATLAB (9.4), Signal Processing Toolbox (8.0), Statistics and Machine Learning Toolbox (11.3), and Curve Fitting Toolbox (3.5.7).
- Keyword:
- Brain-machine interface, Prosthesis, and Upper extremity
- Citation to related publication:
- Nason, S.R., Mender, M.J., Vaskov, A.K., Willsey, M.S., Ganesh Kumar, N., Kung, T.A., Patil, P.G., and Chestek, C.A. (2021). Real-Time Linear Prediction of Simultaneous and Independent Movements of Two Finger Groups Using an Intracortical Brain-Machine Interface. Neuron (accepted).
- Discipline:
- Engineering
-
- Creator:
- Nason, Samuel R., Vaskov, Alex K., Willsey, Matthew S., Welle, Elissa J., An, Hyochan, Vu, Philip P., Bullard, Autumn J., Nu, Chrono S., Kao, Jonathan C., Shenoy, Krishna V., Jang, Taekwang, Kim, Hun-Seok, Blaauw, David, Patil, Parag G., and Chestek, Cynthia A.
- Description:
- This data is a subset of the data used to generate figures similar to figures 1, 2, 3, and 4 in Nason et al., 2020, Nature Biomedical Engineering. The purpose of the study was to demonstrate the benefits of using spiking band power, a low-power but single unit specific recording signal, for brain-machine interfaces with nonhuman primates with the potential to impact low-power brain-machine interfaces with humans. All of the data is contained in .mat files, which can be commonly opened by Matlab and the Python scipy library.
- Keyword:
- Brain-machine interface, Prosthesis, and Neural recording
- Citation to related publication:
- Nason, S.R., Vaskov, A.K., Willsey, M.S., Welle, E.J., An, H., Vu, P.P., Bullard, A.J., Nu, C.S., Kao, J.C., Shenoy, K.V., Jang, T., Kim, H.-S., Blaauw, D., Patil, P.G., and Chestek, C.A. (2020). A low-power band of neuronal spiking activity dominated by local single units improves the performance of brain–machine interfaces. Nat. Biomed. Eng. 4, 973–983. https://doi.org/10.1038/s41551-020-0591-0
- Discipline:
- Engineering
-
- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data repository includes the quantitative features of high frequency, intracranial EEG along with all necessary scripts to reproduce the figures of the accompanying manuscript.
- Keyword:
- high frequency oscillation, HFO, high frequency activity, and epilepsy
- Citation to related publication:
- (under review)
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Mohtat, Peyman, Siegel, Jason B., Stefanopoulou, Anna G., and Lee, Suhak
- Description:
- The focus of this research effort is to systematically study the capability of aging diagnostics using cell expansion under variety of aging conditions and states. The data collection campaign is very important to cover various degradation modes to extract the degradation features that will be used to inform, parameterize, and validate the models developed earlier. In the data collection campaign, we are documenting the evolution of the electrical and mechanical characteristics and especially the reversible mechanical measurement. It is important to note that we collect data using newly developed fixtures that enables the simultaneous measurement of mechanical and electrical response under pseudo-constant pressure.
- Keyword:
- Lithium-ion batteries, Mechanical response, Aging, NMC, and Pouch cells
- Citation to related publication:
- Peyman Mohtat et al. (2021). Reversible and Irreversible Expansion of Lithium-ion Batteries Under a Wide Range of Stress Factors. J. Electrochem. Soc. 168 100520 https://doi.org/10.1149/1945-7111/ac2d3e
- Discipline:
- Engineering
-
- Creator:
- Pine, Alexandra F and Love, Brian J
- Description:
- This data is from a project concerned with dehydrating samples of saturated superabsorbent polymer using a centrifuge. The goal was to consider centrifugation as an energy efficient scheme to dehydrate SAP with the notion of reusing it. The data provided contains mass fractions of solvent removed through centrifugation with varied parameters.
- Keyword:
- Superabsorbent Polymer
- Citation to related publication:
- Pine, A., Wu, C. C., Raghavan, S., & Love, B. (2021). The efficiency of dehydrating desiccants by centrifugation: An assessment of superabsorbent polymers. Drying Technology, 0(0), 1–8. https://doi.org/10.1080/07373937.2021.1939710
- Discipline:
- Engineering
-
- Creator:
- Agnit Mukhopadhyay
- Description:
- Conducting quantitative metrics-based performance analysis of first-principles-based global magnetosphere models is an essential step in understanding their capabilities and limitations, and providing scope for improvements in order to enhance their space weather prediction capabilities for a range of solar conditions. In this study, a detailed comparison of the performance of three global magnetohydrodynamic (MHD) models in predicting the Earth’s magnetopause location and ionospheric cross polar cap potential (CPCP) has been presented. Using the Community Coordinated Modeling Center’s Run-on-Request system and extensive database on results from various magnetospheric scenarios simulated for a variety of solar wind conditions, the aforementioned model predictions have been compared for magnetopause standoff distance estimations obtained from six empirical models, and with cross polar cap potential estimations obtained from the Assimmilative Mapping of Ionospheric Electrodynamics (AMIE) Model and the Super Dual Auroral Radar Network (SuperDARN) observations. We have considered a range of events spanning different space weather activity to analyze the performance of these models. Using a fit performance metric analysis for each event, we have quantified the models’ reproducibility of magnetopause standoff distances and CPCP against empirically-predicted observations, and identified salient features that govern the performance characteristics of the modeled magnetospheric and ionospheric quantities.
- Citation to related publication:
- Mukhopadhyay, A., Jia, X., Welling, D. T., & Liemohn, M. W. (2021). Global Magnetohydrodynamic Simulations: Performance Quantification of Magnetopause Distances and Convection Potential Predictions. Frontiers in Astronomy and Space Sciences, 8. https://doi.org/10.3389/fspas.2021.637197
- Discipline:
- Engineering and Science
-
- Creator:
- Zhang, Kaihua and Collette, Matthew D.
- Description:
- This Ph.D. research focuses on two subject areas: experimental and numerical model, which serves as two essential parts of a digital twin. A digital twin contains models of real-world structures and fuses data from observations of the structures and scale experiment to pull the models into better agreement with the real world. Digital twin models have the promise of representing complex marine structures and providing enhanced lifecycle performance and risk forecasts. Experimentally verifying the updating approaches is necessary but rarely performed. Thus, the proposed work is designing an experiment and developing a numerical model updated by the experimental data. The dataset contains all the data collected in the experiment of a four-crack hexagon- shaped specimen is presented, designed to mimic many of the properties of complex degrading marine structural systems, such as crack interaction, component inter- dependence, redundant load path, and non-binary failure.
- Keyword:
- System Reliability, Dynamic Bayesian Networks, Fatigue Experiment, Crack Length Measurement, Experimental Validation, Reliability Prediction
- Citation to related publication:
- "Evaluating Crack Growth Prediction in Structural Systems with Dynamic Bayesian Networks", submitted to Computers and Structure and Zhang, K., & Collette, M. (2021). Experimental investigation of structural system capacity with multiple fatigue cracks. Marine Structures, 78, 102943. https://doi.org/10.1016/j.marstruc.2021.102943
- Discipline:
- Engineering
-
- Creator:
- Brandt, Daniel, A., Bussy-Virat, Charles, D., and Ridley, Aaron, J.
- Description:
- The Multifaceted Optimization Algorithm (MOA) is a tool for generating corrected empirical model thermospheric densities during geomagnetic storms. It consists of a suite of Python functions that operate around the Spacecraft Orbit Characterization Kit (SpOCK), an orbital propagator developed by Charles D. Bussy-Virat, PhD, Joel Getchius, and Aaron J. Ridley, PhD at the University of Michigan, and it estimates new densities for the NRLMSISE-00 atmospheric model. MOA generates new model densities by estimating modifications to inputs to the NLRMSISE-00 model that minimize the orbit error between modeled spacecraft in SpOCK, and their actual altitudes as described in publicly-available Two-Line Element Sets (TLEs), made available online via Space-track.org. MOA consists of three sub-process: (1) The Area Optimization Algorithm (AROPT), (2) the F10.7 Optimization Algorithm (FOPT), and (3) the Ap Optimization Algorithm (APOPT). AROPT computes the contribution to the drag of the modeled spacecraft due to their varying projected area. FOPT estimates modifications to the 10.7 cm solar radio flux in NRLMSISE-00, and APOPT estimates modifications to the Earth's magnetic activity in NRLMSISE-00. MOA finds these modifications across many spacecraft, and the medians of those modifications are then applied in NLRMSISE-00 along the orbit of another satellite to generate new densities for verification. In this instance, modifications are applied along the orbits of the Swarm spacecraft and compared to Swarm GPS-derived densities.
- Keyword:
- Orbit, Satellite, Two-line Element Set, Thermosphere, and Drag
- Citation to related publication:
- Brandt, D. A., Bussy-Virat, C. D., & Ridley, A. J. (2020). A Simple Method for Correcting Empirical Model Densities During Geomagnetic Storms Using Satellite Orbit Data. Space Weather, 18(12), e2020SW002565. https://doi.org/10.1029/2020SW002565
- Discipline:
- Engineering
-
- Creator:
- Attari, Ali
- Description:
- Please refer to the "README.txt" for more details., MATLAB R2018a (Mathworks, Natick, MA, USA) was used to process this data., and Excel (Microsoft Office) was used to store survey data on the comfort of both systems and also to provide absolute and relative intraobserver variablities for the DM device.
- Keyword:
- Digital Manometry
- Citation to related publication:
- Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system Attari A, Chey WD, Baker JR, Ashton-Miller JA (2020) Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system. PLOS ONE 15(9): e0228761. https://doi.org/10.1371/journal.pone.0228761
- Discipline:
- Engineering, Science, and Health Sciences