Dataset Information

Bdellovibrio electron cryotomography tilt-series acquired by continuous tilting

ABSTRACT:

SUBMITTER: Georges Chreifi

PROVIDER: EMPIAR-10225 | biostudies-other |

REPOSITORIES: biostudies-other

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Publications

Rapid tilt-series acquisition for electron cryotomography.

Chreifi Georges G Chen Songye S Metskas Lauren Ann LA Kaplan Mohammed M Jensen Grant J GJ

Journal of structural biology 20190111 2

Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ∼4 nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography wor ...[more]

PMID: 30639925

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Project description:Faster trains require tilting of the cars to counterbalance the centrifugal forces during curves. Motion sensitive passengers, however, complain of discomfort and overt motion sickness. A recent study comparing different control systems in a tilting train, suggested that the delay of car tilts relative to the curve of the track contributes to motion sickness. Other aspects of the motion stimuli, like the lateral accelerations and the car jitters, differed between the tested conditions and prevented a final conclusion on the role of tilt delay. Nineteen subjects were tested on a motorized 3D turntable that simulated the roll tilts during yaw rotations experienced on a tilting train, isolating them from other motion components. Each session was composed of two consecutive series of 12 ideal curves that were defined on the bases of recordings during an actual train ride. The simulated car tilts started either at the beginning of the curve acceleration phase (no-delay condition) or with 3 s of delay (delay condition). Motion sickness was self-assessed by each subject at the end of each series using an analog motion sickness scale. All subjects were tested in both conditions. Significant increases of motion sickness occurred after the first sequence of 12 curves in the delay condition, but not in the no-delay condition. This increase correlated with the sensitivity of motion sickness, which was self-assessed by each subject before the experiment. The second sequence of curve did not lead to a significant further increase of motion sickness in any condition. Our results demonstrate that, even if the speed and amplitude are as low as those experienced on tilting trains, a series of roll tilts with a delay relative to the horizontal rotations, isolated from other motion stimuli occurring during a travel, generate Coriolis/cross-coupling stimulations sufficient to rapidly induce motion sickness in sensitive individuals. The strength and the rapid onset of the motion sickness reported confirm that, even if the angular velocity involved are low, the Coriolis/cross-coupling resulting from the delay is a major factor in causing sickness that can be resolved by improving the tilt timing relative to the horizontal rotation originating from the curve.

Project description:MOTIVATION:Electron tomography (ET) is a widely used technology for 3D macro-molecular structure reconstruction. To obtain a satisfiable tomogram reconstruction, several key processes are involved, one of which is the calibration of projection parameters of the tilt series. Although fiducial marker-based alignment for tilt series has been well studied, marker-free alignment remains a challenge, which requires identifying and tracking the identical objects (landmarks) through different projections. However, the tracking of these landmarks is usually affected by the pixel density (intensity) change caused by the geometry difference in different views. The tracked landmarks will be used to determine the projection parameters. Meanwhile, different projection parameters will also affect the localization of landmarks. Currently, there is no alignment method that takes interrelationship between the projection parameters and the landmarks. RESULTS:Here, we propose a novel, joint method for marker-free alignment of tilt series in ET, by utilizing the information underlying the interrelationship between the projection model and the landmarks. The proposed method is the first joint solution that combines the extrinsic (track-based) alignment and the intrinsic (intensity-based) alignment, in which the localization of landmarks and projection parameters keep refining each other until convergence. This iterative approach makes our solution robust to different initial parameters and extreme geometric changes, which ensures a better reconstruction for marker-free ET. Comprehensive experimental results on three real datasets show that our new method achieved a significant improvement in alignment accuracy and reconstruction quality, compared to the state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION:The main program is available at https://github.com/icthrm/joint-marker-free-alignment. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

Dataset Information

Bdellovibrio electron cryotomography tilt-series acquired by continuous tilting

Publications

Rapid tilt-series acquisition for electron cryotomography.

Similar Datasets

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