scholarly journals Real-time cryo-EM data pre-processing with Warp

2018 ◽  
Author(s):  
Dimitry Tegunov ◽  
Patrick Cramer

The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens is currently largely uncoupled from subsequent data evaluation, correction and processing. Therefore, the acquisition strategy is difficult to optimize during data collection, often leading to suboptimal microscope usage and disappointing results. Here we provide Warp, a software for real-time evaluation, correction, and processing of cryo-EM data during their acquisition. Warp evaluates and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Warp also rapidly corrects micrographs for global and local motion, and estimates the local defocus with the use of novel algorithms. The software further includes a deep learning-based particle picking algorithm that rivals human accuracy to make the pre-processing pipeline truly automated. The output from Warp can be directly fed into established tools for particle classification and 3D image reconstruction. In a benchmarking study we show that Warp automatically processed a published cryo-EM data set for influenza virus hemagglutinin, leading to an improvement of the nominal resolution from 3.9 Å to 3.2 Å. Warp is easy to install, computationally inexpensive, and has an intuitive and streamlined user interface.


Author(s):  
Alan S. Rudolph ◽  
Ronald R. Price

We have employed cryoelectron microscopy to visualize events that occur during the freeze-drying of artificial membranes by employing real time video capture techniques. Artificial membranes or liposomes which are spherical structures within internal aqueous space are stabilized by water which provides the driving force for spontaneous self-assembly of these structures. Previous assays of damage to these structures which are induced by freeze drying reveal that the two principal deleterious events that occur are 1) fusion of liposomes and 2) leakage of contents trapped within the liposome [1]. In the past the only way to access these events was to examine the liposomes following the dehydration event. This technique allows the event to be monitored in real time as the liposomes destabilize and as water is sublimed at cryo temperatures in the vacuum of the microscope. The method by which liposomes are compromised by freeze-drying are largely unknown. This technique has shown that cryo-protectants such as glycerol and carbohydrates are able to maintain liposomal structure throughout the drying process.





2011 ◽  
Author(s):  
Marie Aschehoug ◽  
C. Shah Kabir
Keyword(s):  


Author(s):  
Andrew J. Graettinger ◽  
Thanaporn Supriyasilp ◽  
S. Rocky Durrans


2011 ◽  
Vol 18 (6) ◽  
pp. 568-572 ◽  
Author(s):  
Zhiping Zhao ◽  
Zongli Hu ◽  
Xin Nie ◽  
Lijing Cheng ◽  
Guolin Ding ◽  
...  


Author(s):  
D Spallarossa ◽  
M Cattaneo ◽  
D Scafidi ◽  
M Michele ◽  
L Chiaraluce ◽  
...  

Summary The 2016–17 central Italy earthquake sequence began with the first mainshock near the town of Amatrice on August 24 (MW 6.0), and was followed by two subsequent large events near Visso on October 26 (MW 5.9) and Norcia on October 30 (MW 6.5), plus a cluster of 4 events with MW > 5.0 within few hours on January 18, 2017. The affected area had been monitored before the sequence started by the permanent Italian National Seismic Network (RSNC), and was enhanced during the sequence by temporary stations deployed by the National Institute of Geophysics and Volcanology and the British Geological Survey. By the middle of September, there was a dense network of 155 stations, with a mean separation in the epicentral area of 6–10 km, comparable to the most likely earthquake depth range in the region. This network configuration was kept stable for an entire year, producing 2.5 TB of continuous waveform recordings. Here we describe how this data was used to develop a large and comprehensive earthquake catalogue using the Complete Automatic Seismic Processor (CASP) procedure. This procedure detected more than 450,000 events in the year following the first mainshock, and determined their phase arrival times through an advanced picker engine (RSNI-Picker2), producing a set of about 7 million P- and 10 million S-wave arrival times. These were then used to locate the events using a non-linear location (NLL) algorithm, a 1D velocity model calibrated for the area, and station corrections and then to compute their local magnitudes (ML). The procedure was validated by comparison of the derived data for phase picks and earthquake parameters with a handpicked reference catalogue (hereinafter referred to as ‘RefCat’). The automated procedure takes less than 12 hours on an Intel Core-i7 workstation to analyse the primary waveform data and to detect and locate 3000 events on the most seismically active day of the sequence. This proves the concept that the CASP algorithm can provide effectively real-time data for input into daily operational earthquake forecasts, The results show that there have been significant improvements compared to RefCat obtained in the same period using manual phase picks. The number of detected and located events is higher (from 84,401 to 450,000), the magnitude of completeness is lower (from ML 1.4 to 0.6), and also the number of phase picks is greater with an average number of 72 picked arrival for a ML = 1.4 compared with 30 phases for RefCat using manual phase picking. These propagate into formal uncertainties of ± 0.9km in epicentral location and ± 1.5km in depth for the enhanced catalogue for the vast majority of the events. Together, these provide a significant improvement in the resolution of fine structures such as local planar structures and clusters, in particular the identification of shallow events occurring in parts of the crust previously thought to be inactive. The lower completeness magnitude provides a rich data set for development and testing of analysis techniques of seismic sequences evolution, including real-time, operational monitoring of b-value, time-dependent hazard evaluation and aftershock forecasting.





2021 ◽  
pp. 1-11
Author(s):  
Tingting Zhao ◽  
Xiaoli Yi ◽  
Zhiyong Zeng ◽  
Tao Feng

YTNR (Yunnan Tongbiguan Nature Reserve) is located in the westernmost part of China’s tropical regions and is the only area in China with the tropical biota of the Irrawaddy River system. The reserve has abundant tropical flora and fauna resources. In order to realize the real-time detection of wild animals in this area, this paper proposes an improved YOLO (You only look once) network. The original YOLO model can achieve higher detection accuracy, but due to the complex model structure, it cannot achieve a faster detection speed on the CPU detection platform. Therefore, the lightweight network MobileNet is introduced to replace the backbone feature extraction network in YOLO, which realizes real-time detection on the CPU platform. In response to the difficulty in collecting wild animal image data, the research team deployed 50 high-definition cameras in the study area and conducted continuous observations for more than 1,000 hours. In the end, this research uses 1410 images of wildlife collected in the field and 1577 wildlife images from the internet to construct a research data set combined with the manual annotation of domain experts. At the same time, transfer learning is introduced to solve the problem of insufficient training data and the network is difficult to fit. The experimental results show that our model trained on a training set containing 2419 animal images has a mean average precision of 93.6% and an FPS (Frame Per Second) of 3.8 under the CPU. Compared with YOLO, the mean average precision is increased by 7.7%, and the FPS value is increased by 3.



Sensors ◽  
2021 ◽  
Vol 21 (7) ◽  
pp. 2534
Author(s):  
Oualid Doukhi ◽  
Deok-Jin Lee

Autonomous navigation and collision avoidance missions represent a significant challenge for robotics systems as they generally operate in dynamic environments that require a high level of autonomy and flexible decision-making capabilities. This challenge becomes more applicable in micro aerial vehicles (MAVs) due to their limited size and computational power. This paper presents a novel approach for enabling a micro aerial vehicle system equipped with a laser range finder to autonomously navigate among obstacles and achieve a user-specified goal location in a GPS-denied environment, without the need for mapping or path planning. The proposed system uses an actor–critic-based reinforcement learning technique to train the aerial robot in a Gazebo simulator to perform a point-goal navigation task by directly mapping the noisy MAV’s state and laser scan measurements to continuous motion control. The obtained policy can perform collision-free flight in the real world while being trained entirely on a 3D simulator. Intensive simulations and real-time experiments were conducted and compared with a nonlinear model predictive control technique to show the generalization capabilities to new unseen environments, and robustness against localization noise. The obtained results demonstrate our system’s effectiveness in flying safely and reaching the desired points by planning smooth forward linear velocity and heading rates.



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