scholarly journals DeepLabStream: Closing the loop using deep learning-based markerless, real-time posture detection

Author(s):  
Jens F. Schweihoff ◽  
Matvey Loshakov ◽  
Irina Pavlova ◽  
Laura Kück ◽  
Laura A. Ewell ◽  
...  

AbstractIn general, animal behavior can be described as the neuronal-driven sequence of reoccurring postures through time. Current technologies enable offline pose estimation with high spatio-temporal resolution, however to understand complex behaviors, it is necessary to correlate the behavior with neuronal activity in real-time. Here we present DeepLabStream, a highly versatile, closed-loop solution for freely moving mice that can autonomously conduct behavioral experiments ranging from behavior-based learning tasks to posture-dependent optogenetic stimulation. DeepLabStream has a temporal resolution in the millisecond range, can operate with multiple devices and can be easily tailored to a wide range of species and experimental designs. We employ DeepLabStream to autonomously run a second-order olfactory conditioning task for freely moving mice and to deliver optogenetic stimuli based on mouse head-direction.

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jens F. Schweihoff ◽  
Matvey Loshakov ◽  
Irina Pavlova ◽  
Laura Kück ◽  
Laura A. Ewell ◽  
...  

AbstractIn general, animal behavior can be described as the neuronal-driven sequence of reoccurring postures through time. Most of the available current technologies focus on offline pose estimation with high spatiotemporal resolution. However, to correlate behavior with neuronal activity it is often necessary to detect and react online to behavioral expressions. Here we present DeepLabStream, a versatile closed-loop tool providing real-time pose estimation to deliver posture dependent stimulations. DeepLabStream has a temporal resolution in the millisecond range, can utilize different input, as well as output devices and can be tailored to multiple experimental designs. We employ DeepLabStream to semi-autonomously run a second-order olfactory conditioning task with freely moving mice and optogenetically label neuronal ensembles active during specific head directions.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sergey Zayko ◽  
Ofer Kfir ◽  
Michael Heigl ◽  
Michael Lohmann ◽  
Murat Sivis ◽  
...  

AbstractLight-induced magnetization changes, such as all-optical switching, skyrmion nucleation, and intersite spin transfer, unfold on temporal and spatial scales down to femtoseconds and nanometers, respectively. Pump-probe spectroscopy and diffraction studies indicate that spatio-temporal dynamics may drastically affect the non-equilibrium magnetic evolution. Yet, direct real-space magnetic imaging on the relevant timescales has remained challenging. Here, we demonstrate ultrafast high-harmonic nanoscopy employing circularly polarized high-harmonic radiation for real-space imaging of femtosecond magnetization dynamics. We map quenched magnetic domains and localized spin structures in Co/Pd multilayers with a sub-wavelength spatial resolution down to 16 nm, and strobosocopically trace the local magnetization dynamics with 40 fs temporal resolution. Our compact experimental setup demonstrates the highest spatio-temporal resolution of magneto-optical imaging to date. Facilitating ultrafast imaging with high sensitivity to chiral and linear dichroism, we envisage a wide range of applications spanning magnetism, phase transitions, and carrier dynamics.


2019 ◽  
Author(s):  
Hanna Meyer ◽  
Marwan Katurji ◽  
Florian Detsch ◽  
Fraser Morgan ◽  
Thomas Nauss ◽  
...  

Abstract. Air temperature is an important baseline parameter for terrestrial Antarctica in the context of patterns and processes in climatology, hydrology or ecology. There are still large uncertainties on how the Antarctic system responds to spatio-temporal variability of temperature. This can partly be attributed to the lack of high resolution datasets. In this paper, we present AntAir, a new dataset of gridded air temperatures in 1 km spatial and daily temporal resolution that is available since 2003. AntAir was created by modelling daily air temperature from MODIS land surface temperature using machine learning algorithms. Data from 70 weather stations was used as a reference. Daily temperatures could be estimated with a R2 of 0.91 and a RMSE of 5.07 °C validated on independent years. The performance to estimate the time series of a new spatial location was R2 = 0.78 and RMSE = 5.83 °C. Hence the high spatial and temporal resolution of the dataset as well as the high accuracy make AntAir an important baseline dataset for a wide range of applications in environmental science of Antarctica. The dataset is available at https://doi.pangaea.de/10.1594/PANGAEA.902166 (daily, Meyer et al., 2019a) and https://doi.pangaea.de/10.1594/PANGAEA.902193 (monthly, Meyer et al., 2019b).


Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 598
Author(s):  
Massimiliano Pau ◽  
Bruno Leban ◽  
Michela Deidda ◽  
Federica Putzolu ◽  
Micaela Porta ◽  
...  

The majority of people with Multiple Sclerosis (pwMS), report lower limb motor dysfunctions, which may relevantly affect postural control, gait and a wide range of activities of daily living. While it is quite common to observe a different impact of the disease on the two limbs (i.e., one of them is more affected), less clear are the effects of such asymmetry on gait performance. The present retrospective cross-sectional study aimed to characterize the magnitude of interlimb asymmetry in pwMS, particularly as regards the joint kinematics, using parameters derived from angle-angle diagrams. To this end, we analyzed gait patterns of 101 pwMS (55 women, 46 men, mean age 46.3, average Expanded Disability Status Scale (EDSS) score 3.5, range 1–6.5) and 81 unaffected individuals age- and sex-matched who underwent 3D computerized gait analysis carried out using an eight-camera motion capture system. Spatio-temporal parameters and kinematics in the sagittal plane at hip, knee and ankle joints were considered for the analysis. The angular trends of left and right sides were processed to build synchronized angle–angle diagrams (cyclograms) for each joint, and symmetry was assessed by computing several geometrical features such as area, orientation and Trend Symmetry. Based on cyclogram orientation and Trend Symmetry, the results show that pwMS exhibit significantly greater asymmetry in all three joints with respect to unaffected individuals. In particular, orientation values were as follows: 5.1 of pwMS vs. 1.6 of unaffected individuals at hip joint, 7.0 vs. 1.5 at knee and 6.4 vs. 3.0 at ankle (p < 0.001 in all cases), while for Trend Symmetry we obtained at hip 1.7 of pwMS vs. 0.3 of unaffected individuals, 4.2 vs. 0.5 at knee and 8.5 vs. 1.5 at ankle (p < 0.001 in all cases). Moreover, the same parameters were sensitive enough to discriminate individuals of different disability levels. With few exceptions, all the calculated symmetry parameters were found significantly correlated with the main spatio-temporal parameters of gait and the EDSS score. In particular, large correlations were detected between Trend Symmetry and gait speed (with rho values in the range of –0.58 to –0.63 depending on the considered joint, p < 0.001) and between Trend Symmetry and EDSS score (rho = 0.62 to 0.69, p < 0.001). Such results suggest not only that MS is associated with significantly marked interlimb asymmetry during gait but also that such asymmetry worsens as the disease progresses and that it has a relevant impact on gait performances.


Sign in / Sign up

Export Citation Format

Share Document