Dataset Information

TEM image restoration from fast image streams.

ABSTRACT: Microscopy imaging experiments generate vast amounts of data, and there is a high demand for smart acquisition and analysis methods. This is especially true for transmission electron microscopy (TEM) where terabytes of data are produced if imaging a full sample at high resolution, and analysis can take several hours. One way to tackle this issue is to collect a continuous stream of low resolution images whilst moving the sample under the microscope, and thereafter use this data to find the parts of the sample deemed most valuable for high-resolution imaging. However, such image streams are degraded by both motion blur and noise. Building on deep learning based approaches developed for deblurring videos of natural scenes we explore the opportunities and limitations of deblurring and denoising images captured from a fast image stream collected by a TEM microscope. We start from existing neural network architectures and make adjustments of convolution blocks and loss functions to better fit TEM data. We present deblurring results on two real datasets of images of kidney tissue and a calibration grid. Both datasets consist of low quality images from a fast image stream captured by moving the sample under the microscope, and the corresponding high quality images of the same region, captured after stopping the movement at each position to let all motion settle. We also explore the generalizability and overfitting on real and synthetically generated data. The quality of the restored images, evaluated both quantitatively and visually, show that using deep learning for image restoration of TEM live image streams has great potential but also comes with some limitations.

SUBMITTER: Wieslander H

PROVIDER: S-EPMC7850474 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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TEM image restoration from fast image streams.

Wieslander Håkan H Wählby Carolina C Sintorn Ida-Maria IM

PloS one 20210201 2

Microscopy imaging experiments generate vast amounts of data, and there is a high demand for smart acquisition and analysis methods. This is especially true for transmission electron microscopy (TEM) where terabytes of data are produced if imaging a full sample at high resolution, and analysis can take several hours. One way to tackle this issue is to collect a continuous stream of low resolution images whilst moving the sample under the microscope, and thereafter use this data to find the parts ...[more]

PMID: 33524053

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Project description:To investigate the undesired irradiations outside of the treatment field by electron streams in air (air-electron-stream) during magnetic-resonance image-guided radiation therapy (MR-IGRT). A custom-made support phantom adjusting angles between the beam central axis (CAX) and the phantom surface (termed phantom-angles), were used. Using the ViewRay system, a rectangular parallelepiped phantom placed on the support phantom, was irradiated with field sizes of 6.3 cm × 6.3 cm (FS6.3) and 12.6 cm × 12.6 cm (FS12.6) at gantry angles of 0°, 30°, and 330°, and phantom-angles of 10°, 20°, and 30°. For each beam delivery, the isocenter was located at the center of mass of the phantom and 3 Gy was delivered to the isocenter (prescription dose = 3 Gy). The doses given by the air-electron-streams were measured using the EBT3 films on the panels placed orthogonal to the direction of the magnetic field at distances of 10 and 17 cm from CAX. Two dose distributions per irradiation were measured on the panel facing the phantom surface of the incident beam (front panel) and on the panel facing the phantom surface of the beam exit (end panel). We investigated the doses by the air-electron-streams by calculating the average doses inside the circles drawn around a point of the maximum dose with radii of x cm (DRx) from the dose distributions on the panels (x = 1-5 cm). The largest value of DRx was DR1 (1.64 Gy, 55% of the prescription dose) at 10 cm distance from CAX, with FS12.6, at 30° phantom-angle and 330° gantry angle. The average difference of the DR1 at the end panels (FS12.6) between the calculations and measurements was 1.36 Gy. The average global gamma passing rate with 3%/3 mm on the dose distributions at the end panels (FS12.6) was 40.3%. The calculated dose distributions on both panels were not coincident with the measured dose distributions. The Spearman's rank correlation coefficients between the projected areas and the DRx values were always higher than 0.75 (all with p < 0.001). The doses by the air-electron-streams increased with the projected areas of the cross-sections of the treatment beams on the panels.

Dataset Information

TEM image restoration from fast image streams.

Publications

TEM image restoration from fast image streams.

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