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At least 19 records

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗

A self-supervised workflow for particle picking in cryo-EM

High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as Relion , cryoSPARC , cisTEM , SPHIRE and EMAN2 .

2D class averages↗

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗

Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges

Abstract Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of high-resolution 3-Dimensional (3D) structures of large biological macromolecules. Protein particle picking, the process of identifying individual protein particles in cryo-EM micrographs for building protein structures, has progressed from manual and template-based methods to sophisticated artificial intelligence (AI)-driven approaches in recent years. This review critically examines the evolution and current state of cryo-EM particle picking methods, with an emphasis on the impact of AI. We conducted a comparative evaluation of popular AI-based particle picking methods, using both general machine learning metrics and specific cryo-EM structure determination metrics. This analysis involved constructing the 3D density map from the picked protein particles and assessing the obtained resolution and particle orientation diversity, underscoring the significant impact of AI on cryo-EM particle picking. Despite the advancements, we also identified key obstacles, such as handling complex micrographs with small proteins. The analysis provides insights into the future development of more sophisticated and fully automated AI methods in cryo-EM particle recognition.

Biochemistry & Molecular Biology↗

CryoTransformer: a transformer model for picking protein particles from Cryo-EM micrographs

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structures from them. However, the widely used template-based particle picking process requires some manual particle picking and is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) can potentially automate particle picking, the current AI methods pick particles with low precision or low recall. The erroneously picked particles can severely reduce the quality of reconstructed protein structures, especially for the micrographs with low signal-to-noise-ratio (SNR).

59 BASIC BIOLOGICAL SCIENCES↗

Model-based Reconstruction for Single Particle Cryo-Electron Microscopy

Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where there may not be sufficient data corresponding to each class to obtain an accurate reconstruction using standard algorithms. In this paper we present a model-based image reconstruction technique that uses a regularized cost function to reconstruct the 3D density map by assuming known orientations for the particles. Our method casts the reconstruction as minimizing a cost function involving a novel forward model term that accounts for the contrast transfer function of the microscope, the orientation of the particles and the center of rotation offsets. We combine the forward model term with a regularizer that enforces desirable properties in the volume to be reconstructed. Using simulated data, we demonstrate how our method can significantly improve upon the typically used approach.

Venkatakrishnan, Singanallur↗

Test particle calculations of pick-up ions in the vicinity of Comet Giacobini-Zinner

Ionization of cometary neutral molecules produces ions which are picked-up by the solar wind. The cometary ion pick-up process for Comet Giacobini-Zinner is studied using a test particle method in which trajectories are numerically calculated for several thousand ions whose initial locations were chosen randomly with probability proportional to the neutral density. The cometary ion distribution function was calculated at several locations upstream of the bow shock. Several types of magnetic fluctuations were included. Circularly and linearly polarized monochromatic waves result in less pitch-angle scattering of pick-up ions than turbulent fluctuations which have about the same amplitude. Some anisotropy remains in the distribution function just upstream of the shock, even for the turbulent fluctuations.

Cravens, T. E.↗

Monte Carlo simulation of particle acceleration at astrophysical shocks

A Monte Carlo code was developed for the simulation of particle acceleration at astrophysical shocks. The code is implemented in Turbo Pascal on a PC. It is modularized and structured in such a way that modification and maintenance are relatively painless. Monte Carlo simulations of particle acceleration at shocks follow the trajectories of individual particles as they scatter repeatedly across the shock front, gaining energy with each crossing. The particles are assumed to scatter from magnetohydrodynamic (MHD) turbulence on both sides of the shock. A scattering law is used which is related to the assumed form of the turbulence, and the particle and shock parameters. High energy cosmic ray spectra derived from Monte Carlo simulations have observed power law behavior just as the spectra derived from analytic calculations based on a diffusion equation. This high energy behavior is not sensitive to the scattering law used. In contrast with Monte Carlo calculations diffusive calculations rely on the initial injection of supra-thermal particles into the shock environment. Monte Carlo simulations are the only known way to describe the extraction of particles directly from the thermal pool. This was the triumph of the Monte Carlo approach. The question of acceleration efficiency is an important one in the shock acceleration game. The efficiency of shock waves efficient to account for the observed flux of high energy galactic cosmic rays was examined. The efficiency of the acceleration process depends on the thermal particle pick-up and hence the low energy scattering in detail. One of the goals is the self-consistent derivation of the accelerated particle spectra and the MHD turbulence spectra. Presumably the upstream turbulence, which scatters the particles so they can be accelerated, is excited by the streaming accelerated particles and the needed downstream turbulence is convected from the upstream region. The present code is to be modified to include a better description of particle scattering (pitch-angle instead of hard-sphere) and as iterative procedure for treating the self-excitation of the MHD turbulence.

Campbell, Roy K.↗

Closure models for the feedback of energetic particles on plasma turbulence

Energetic particles interact with the plasma surrounding them, resonating with certain types of plasma waves to stabilize them while destabilizing others, and changing the character of the background turbulence in ways that have not been fully quantified or understood. Interaction with the turbulent background plasma is key to the acceleration of many types of energetic particles including high-energy cosmic rays, solar energetic particles, and pick-up ions. The acceleration of particles is a process that would ideally be described by a kinetic model, a type of model that follows a probability distribution function (PDF) for all particles in 7-dimensional (x, y, z, v x , v y , v z , t) space. Because of the high dimensionality of a kinetic model, simulations that solve kinetic equations use the largest computational resources currently available, and are yet unable to simulate a realistic number of particles, reach the large scales necessary for astrophysical problems, and use high-precision numerical methods. Two available alternatives to kinetic plasma models have been explored for this problem, with limited success. One is a multi-fluid model produced by a cumulant discarding closure, which evolves coupled equations for the velocity, magnetic field, and internal energy for both the background plasma and the fluid of energetic particles. However, simulations that solve multi-fluid magnetohydrodynamic (MHD) equations are able to include the interaction with energetic particles only in crude ways, typically as an add-on pressure term. The second alternative is to use a hybrid method to couple a fluid description of the background plasma to a kinetic model or a Fokker–Planck model for the energetic particles. These methods are hampered by the physical modeling of the coupling. In this work, we develop a new model, which follows the PDF for all particles; this can be viewed as a step toward physical realism above a multi-fluid MHD model, while also being more computationally efficient than a kinetic model. The equations we develop model both the background plasma and the energetic particles self-consistently. Over the last decade, similar PDF methods have been developed to a high level of sophistication to model reactive flows and turbulent combustion for engineering applications. For treatment of the feedback of the energetic particles on a background plasma, a PDF closure approach should evaluate the mean characteristics, including the density, with better statistical quality than will particle-sampling procedures.

79 ASTRONOMY AND ASTROPHYSICS↗

Origin and maintenance of the oxygen torus in Saturn's magnetosphere

Observations of thermal ions in Saturn's inner magnetosphere suggest distributed local sources rather than diffusive mass loading from a source located further out. We suggest that the plasma is produced and maintained mainly by 'self-sputtering' of E ring dust. Sputtered particles are 'picked up' by the planetary magnetospheric field and accelerated to corotation energies (of the order of 8 eV/amu). The sputter yield for oxygen on ice at, for example, 120 eV is about 5, which implies that an avalanche of self-sputtering occurs. The plasma density is built up until it is balanced by local losses, presumably pitch angle scattering into the loss cone and absorption in the planet's ionosphere. The plasma density determines the distribution of dust in the E ring through plasma drag. Thus a feedback mechanism between the plasma and the E ring dust is established. The model accounts for the principal plasma observations and simultaneously the radial optical depth profile of the E ring.

Morfill, G. E.↗

Particle-impact noise detector (PIND)

Package, in page assembly, is subjected to low-frequency vibration, and noise generated by particle impacts is picked up by transducer. Test procedure calls for three transverse shocks to be applied to page to dislodge any trapped particles.

Barr, R. J.↗

Analysis of Cosmic Spherule Candidates from the Kwajalein Micrometeorite Collection

The Kwajalein micrometeorite collection utilised high volume air samplers fitted with 5 micrometer laser-etched polycarbonate membrane filters to capture particles directly from the atmosphere. The filters were changed weekly over several months throughout 2011/12, providing the opportunity to investigate the contemporary flux of micrometeorites. We recently reported the results of our initial survey of cosmic spherule-like particles on several of these filters. We identified three main groups of particle based on bulk compositions: 1. Silicate spherules rich in Mg, Ca and Fe, 2. Silicate spherules rich in Al, Ca, K and/or Na and 3. Fe-rich spherules. Abundances appeared to change over time suggesting links with celestial activity (e.g. meteor showers), however, spherules similar to groups 2 and 3 can be produced by terrestrial and anthropogenic activity (e.g. volcanic microspherules exhibit similar compositions to group 2 spherules and metallic spherules similar to those of group 3 can be formed during fuel combustion). We are now studying the internal structures and chemistries of these spherules and comparing against cosmic spherules identified in other collections to confrim their origins and further contrain the contemporary micrometeorite flux. Particles are being picked, embedded in resin and polished through to reveal their interiors. Here we will describe our ongoing analyses of these particles via SEM. We will also introduce our new collection using this method that is currently being performed in the Antarctic.

Wozniakiewicz, P. J.↗

Pick-Up Ion Instabilities at Planetary Magnetospheres

This effort involved the analysis of low frequency waves as observed by the Galileo spacecraft near the Galilean moon, Io. Io is a significant source of material, especially SO2, and various products of dissociation, and further these atoms and molecules are readily ionized. The initial velocity of the ions is essentially that of the neutral species, i.e., the Keplerian velocity. The plasma, on the other hand is co-rotating, and there is a differential flow of the order 57 km/s between the plasma and the neutral particles. Thus pick-up ion instabilities are Rely to occur within the Jovian magnetosphere. Indeed, magnetometer observations from the Galileo spacecraft clearly show ion cyclotron waves that have been identified with a large variety of plasma species, such as O+, S++ (which has the same gyro-frequency as O+), S+, and SO2+. Typically, however, the dominant frequency is near the SO2+ gyro-frequency. The research effort was originally planned to be a team effort between Robert J. Strangeway as the Principal Investigator, and Debbie Huddleston, who was an Assistant Research Geophysicist at UCLA. Unfortunately, Dr. Huddleston took a position within Industry. The effort was therefore descoped, and Dr. Strangeway instead pursued a collaboration with Dr. Xochitl Blanco-Cano, of the Instituto de Geofisica, Universidad Nacional Autonoma de Mexico. This has proved to be a productive collaboration, with several papers and publications arising out of the effort. The magnetic field oscillations near lo generally fall into two types: ion cyclotron waves, with frequencies near an ion gyro-frequency, and lower frequency mirror-mode waves. The ion cyclotron waves are mainly transverse, and frequently propagate along the ambient magnetic field. The mirror-mode waves are compressional waves, and they have essentially zero frequency in the plasma rest frame. One of the purposes of our investigation is to understand what controls the types of wave modes that occur, since both wave modes can be drive unstable by the pressure anisotropy associated with the pick up ions. The pick ion velocity is perpendicular to the ambient magnetic field, and is generally much larger than the thermal velocity, at least initially. At its simplest, we found that the ion cyclotron waves are controlled by the parameters of the species in gyro-resonance with the wave. Thus, while the growth rates for the lower mass (higher gyro-frequency) pick-up ions are generally larger, we found that the heavier SO2+ ion cyclotron waves are generally preferred. This is because one of the effects of the wave instability is to diffuse the ions in pitch angle and energy. The lower mass ions therefore consist of both a ring of recently created pick-up ions, and a thermal background. This thermal background quenches the ion cyclotron instability. SO2+ is different, however. Being a molecule, the species can also dissociate. Our analysis suggests that the dissociation acts on a time scale comparable to or faster than the velocity space diffusion time scale. There are consequently no thermal SO2+ ions to quench the instability. We have also investigated the mirror-mode. This mode can at times grow more rapidly than the individual ion cyclotron waves. This is mainly because the mirror-mode can grow off the pressure anisotropy of the individual species with which the waves are in resonance. Lastly, as part of this effort we have begun to investigate the instability for obliquely propagating modes. Galileo observations show that at times the ion cyclotron waves are significantly elliptically polarized, and further the wave vector is at a large angle to the field, significant growth can occur for oblique propagation. Depending on the group velocity of the waves, it is possible that obliquely propagating modes have higher advective growth rate, but this has yet to be determined.

Strangeway, Robert J.↗

Technique for pinpointing submicron particles in the electron microprobe

Series of electron micrographs at successively lower magnifications can localize the substrate area sufficiently for a particle to be picked up by the beam of the electron microprobe. This approach could be modified to apply to fractographic studies, particularly of oxidation products stripped from fractures.

Miller, E. L.↗

Finite Larmor radius effect on ion pickup at Venus

The interaction of the solar wind with Venus is influenced by the pickup of newly born exospheric oxygen ions by the convecting magnetosheath plasma. The flow and field configuration of the magnetosheath plasma, together with the large gyroradius of the pickup ions, cause mass loading to occur preferentially on one side of the magnetosheath. The observed hemispherical asymmetry in the magnetic field in the near-planet magnetosheath, attributed to this pickup process, is confirmed by direct observation of the picked-up planetary particles. Test particle calculations show that a current system created by ion pickup has the appropriate location and magnitude to account for the magnetic field asymmetry. The results indicate that a fluid treatment of the Venus mass-loading problem is not entirely appropriate; a hybrid or kinetic model is necessary to incorporate the finite Larmor radius of the pickup particles which produces the observed asymmetry.

Phillips, J. L.↗

On the flux and the energy spectrum of interstellar ions in the solar system

The flux density of ions created by ionization of interstellar neutral particles in the solar system and picked up by the solar wind is calculated as a function of the neutral particles. For atomic hydrogen the flux density is estimated to exceed 10,000/sq cm/sec over the distance range from a few to nearly 100 AU. The velocity space distribution of the interstellar ions is calculated under the assumption of no significant energy diffusion but with inclusion of adiabatic effects as well as a possible strong pitch angle diffusion. The energy spectrum is highly nonthermal and much broader than that of the solar wind ions; interstellar protons are easily distinguishable from solar wind protons by their location in velocity space. If charge exchange is an important contributor to the ionization of hydrogen, the observed local intensity of interstellar protons should exhibit time variations correlated with the density changes of the solar wind stream structure.

Vasyliunas, V. M.↗

Loss of Water from Saturn's E-Ring Through Ion Pick-Up

One of the possible loss processes for Saturn s E-ring is ionization followed by acceleration by the electric field associated with the corotating magnetized plasma. It is possible to determine if this process is occurring by detecting electromagnetic waves at the gyrofrequency of water group ions. If the energy the particle gains in this pick-up process is sufficiently great, the picked up ions will generate ion cyclotron waves. Pioneer 11 and Voyager 1 both observed intervals of such waves associated with water group ions during their passes through Saturn s E-ring. Presently the magnetometer onboard the Cassini spacecraft is also seeing water group ion cyclotron oscillations. The Cassini data allow the spatial and temporal behavior of the waves to be mapped in ways not possible during the previous flybys. Analyses of these waves allow us to study the rate of mass loading and its latitudinal and local time variation. In conjunction with previous data, we can then determine the variation as the inclination of the ring to the Sun changes, in accordance with Saturn's seasons. These waves may be the clue to how Saturn powers its magnetosphere as the newly born ions could be the driver for the radial motion of the plasma and to how the E-ring may play the equivalent role to that of Io in the jovian magnetosphere.

Leisner, J. S.↗

Surface Exposure History of Asteroid Bennu Based on Cosmogenic Radionuclides in OSIRIS-Rex Samples

The surface of asteroid Bennu changes over time because of impacts, mass movement, and particle ejections [1-4]. The OSIRIS-REx samples were collected from a 20-m-diameter crater on Bennu called Hokioi. One of the driving hypotheses of the mission is that Hokioi is part of a population of small (<25 m) craters that are less than 0.1 Myr old and contain relatively unweathered material [1,4]. Our goal is to understand the recent surface exposure history of Bennu, utilizing radionuclides (10Be, 26Al, 36Cl, 41Ca) produced by both galactic and solar cosmic rays. We received ~12 mg of aggregate sample OREX-803014-0. We picked five of the larger particles with masses ranging from 0.24 to 0.68 mg. We dissolved each particle, along with 0.15 mg Be and 1.0 mg Cl carrier, in HF/HNO3 mixture, and did the same for the remaining aggregate sample of 9.8 mg. After dissolution, we took a small aliquot for chemical analysis, added 0.7 mg of Al carrier, and separated Be, Al, and Cl for analysis of cosmogenic 10Be, 26Al, and 36Cl by accelerator mass spectrometry [5]. Preliminary 26Al results show concentrations of 21–27 dpm/kg for the Bennu samples, with an average of 22.5 ± 0.6 dpm/kg for the five particles and 21.1 ± 0.7 dpm/kg for the remaining aggregate. These values are close to the expected 26Al saturation values of 25–30 dpm/kg for the top 1 m of Bennu’s regolith, suggesting a minimum exposure age of 1.5–2.0 Myr near the surface. Our initial Bennu results also resemble those found for Ryugu samples [6,7]; thus, we can hypothesize that the two asteroids have had similar surface exposure histories.

K C Welten↗