Resolution Of 3D Reconstruction Research Articles

Full-Volume 3D Fluid Flow Reconstruction With Light Field PIV.

Particle Imaging Velocimetry (PIV) is a classical method that estimates fluid flow by analyzing the motion of injected particles. To reconstruct and track the swirling particles is a difficult computer vision problem, as the particles are dense in the fluid volume and have similar appearances. Further, tracking a large number of particles is particularly challenging due to heavy occlusion. Here we present a low-cost PIV solution that uses compact lenslet-based light field cameras as imaging device. We develop novel optimization algorithms for dense particle 3D reconstruction and tracking. As a single light field camera has limited capacity in resolving depth (z-dimension measurement), the resolution of 3D reconstruction on the x-y plane is much higher than along the z-axis. To compensate for the imbalanced resolution in 3D, we use two light field cameras positioned at an orthogonal angle to capture particle images. In this way, we can achieve high-resolution 3D particle reconstruction in the full fluid volume. For each time frame, we first estimate particle depths under a single viewpoint by exploiting the focal stack symmetry of light field. We then fuse the recovered 3D particles in two views by solving a linear assignment problem (LAP). Specifically, we propose an anisotropic point-to-ray distance as matching cost to handle the resolution mismatch. Finally, given a sequence of 3D particle reconstructions over time, we recover the full-volume 3D fluid flow with a physically-constrained optical flow, which enforces local motion rigidity and fluid incompressibility. We perform comprehensive experiments on synthetic and real data for ablation and evaluation. We show that our method recovers full-volume 3D fluid flows of various types. Two-view reconstruction results achieves higher accuracy than those with one view only.

An electron counting algorithm improves imaging of proteins with low-acceleration-voltage cryo-electron microscope

Relative to the 300-kV accelerating field, electrons accelerated under lower voltages are potentially scattered more strongly. Lowering the accelerate voltage has been suggested to enhance the signal-to-noise ratio (SNR) of cryo-electron microscopy (cryo-EM) images of small-molecular-weight proteins (<100 kD). However, the detection efficient of current Direct Detection Devices (DDDs) and temporal coherence of cryo-EM decrease at lower voltage, leading to loss of SNR. Here, we present an electron counting algorithm to improve the detection of low-energy electrons. The counting algorithm increased the SNR of 120-kV and 200-kV cryo-EM image from a Falcon III camera by 8%, 20% at half the Nyquist frequency and 21%, 80% at Nyquist frequency, respectively, resulting in a considerable improvement in resolution of 3D reconstructions. Our results indicate that with further improved temporal coherence and a dedicated designed camera, a 120-kV cryo-electron microscope has potential to match the 300-kV microscope at imaging small proteins.

Processing apoferritin with the Appion pipeline.

The 3DEM map challenge provided an opportunity to test different algorithms and workflows for processing single particle cryo-EM data. We were interested in testing whether we could use the standard Appion workflow with minimal manual intervention to achieve similar or better resolution than other challengers. Another question we were interested in testing was what the influence of particle sorting and elimination would be on the resolution and quality of 3D reconstructions. Since apoferritin is historically a challenging particle for single particle reconstruction and the authors of the original map challenge data used only a fraction of the particles present in the dataset, we focused on the apoferritin dataset for our entry. We submitted a 3.7 Å map from 25,844 particles and a 3.6 Å map from 53,334 particles and after assessment were among the best of the apoferritin maps that were submitted. Here we present the details of our reconstruction strategy and compare our strategy to that of another high-scoring apoferritin map. Altogether, our results suggest that for a relatively conformationally homogeneous particle like apoferritin, including as many particles as possible after elimination of junk leads to the highest resolution, and the choice of parameters for custom mask creation can lead to subtle but significant changes in the resolution of 3D reconstructions.

Symmetry-adapted spherical harmonics method for high-resolution 3D single-particle reconstructions

Three-dimensional (3D) reconstruction is the last and an essential step toward high-resolution structural determination in single-particle cryo-electron microscopy (cryoEM). We have implemented a new algorithm for reconstructing 3D structures of macromolecular complexes with icosahedral symmetry from cryoEM images. Icosahedral symmetry-adapted functions (ISAFs) are used to interpolate structural factors in the reciprocal space to generate a 3D reconstruction in spherical coordinates. In our implementation, we introduced a recursive method for deriving higher order ISAFs from three lower order seed functions. We demonstrate improvements of our new method in both the noise suppression and the effective resolution in 3D reconstruction over the commonly used Fourier–Bessel synthesis method introduced by Crowther et al. three decades ago. Our 3D reconstruction method can be extended to macromolecular complexes with other symmetry types and is thus likely to impact future high-resolution cryoEM single-particle reconstruction efforts in general.