skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: On cross-correlations, averages and noise in electron microscopy
Biological samples are radiation-sensitive and require imaging under low-dose conditions to minimize damage. As a result, images contain a high level of noise and exhibit signal-to-noise ratios that are typically significantly smaller than 1. Averaging techniques, either implicit or explicit, are used to overcome the limitations imposed by the high level of noise. Averaging of 2D images showing the same molecule in the same orientation results in highly significant projections. A high-resolution structure can be obtained by combining the information from many single-particle images to determine a 3D structure. Similarly, averaging of multiple copies of macromolecular assembly subvolumes extracted from tomographic reconstructions can lead to a virtually noise-free high-resolution structure. Cross-correlation methods are often used in the alignment and classification steps of averaging processes for both 2D images and 3D volumes. However, the high noise level can bias alignment and certain classification results. While other approaches may be implicitly affected, sensitivity to noise is most apparent in multireference alignments, 3D reference-based projection alignments and projection-based volume alignments. Here, the influence of the image signal-to-noise ratio on the value of the cross-correlation coefficient is analyzed and a method for compensating for this effect is provided.  more » « less
Award ID(s):
1660908
PAR ID:
10092637
Author(s) / Creator(s):
;
Date Published:
Journal Name:
Acta Crystallographica Section F Structural Biology Communications
Volume:
75
Issue:
1
ISSN:
2053-230X
Page Range / eLocation ID:
12 to 18
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; (, BMC Bioinformatics)
    null (Ed.)
    Abstract Background Cryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D density map of a protein structure. However, low contrast and high noise in particle images make it challenging to build 3D density maps at intermediate to high resolution (1–3 Å). To overcome this problem, we propose a fully automated cryo-EM 3D density map reconstruction approach based on deep learning particle picking. Results A perfect 2D particle mask is fully automatically generated for every single particle. Then, it uses a computer vision image alignment algorithm (image registration) to fully automatically align the particle masks. It calculates the difference of the particle image orientation angles to align the original particle image. Finally, it reconstructs a localized 3D density map between every two single-particle images that have the largest number of corresponding features. The localized 3D density maps are then averaged to reconstruct a final 3D density map. The constructed 3D density map results illustrate the potential to determine the structures of the molecules using a few samples of good particles. Also, using the localized particle samples (with no background) to generate the localized 3D density maps can improve the process of the resolution evaluation in experimental maps of cryo-EM. Tested on two widely used datasets, Auto3DCryoMap is able to reconstruct good 3D density maps using only a few thousand protein particle images, which is much smaller than hundreds of thousands of particles required by the existing methods. Conclusions We design a fully automated approach for cryo-EM 3D density maps reconstruction (Auto3DCryoMap). Instead of increasing the signal-to-noise ratio by using 2D class averaging, our approach uses 2D particle masks to produce locally aligned particle images. Auto3DCryoMap is able to accurately align structural particle shapes. Also, it is able to construct a decent 3D density map from only a few thousand aligned particle images while the existing tools require hundreds of thousands of particle images. Finally, by using the pre-processed particle images,Auto3DCryoMap reconstructs a better 3D density map than using the original particle images. 
    more » « less
  2. ; ; ; ; ; ; (, Biological Imaging)
    Abstract Single-particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution three-dimensional (3D) structure of biological macromolecules from many noisy and randomly oriented projection images. One notable approach to 3D reconstruction, known as Kam’s method, relies on the moments of the two-dimensional (2D) images. Inspired by Kam’s method, we introduce a rotationally invariant metric between two molecular structures, which does not require 3D alignment. Further, we introduce a metric between a stack of projection images and a molecular structure, which is invariant to rotations and reflections and does not require performing 3D reconstruction. Additionally, the latter metric does not assume a uniform distribution of viewing angles. We demonstrate the uses of the new metrics on synthetic and experimental datasets, highlighting their ability to measure structural similarity. 
    more » « less
  3. ; ; ; ; ; (, Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies)
    Unsupervised cross-lingual projection for part-of-speech (POS) tagging relies on the use of parallel data to project POS tags from a source language for which a POS tagger is available onto a target language across word-level alignments. The projected tags then form the basis for learning a POS model for the target language. However, languages with rich morphology often yield sparse word alignments because words corresponding to the same citation form do not align well. We hypothesize that for morphologically complex languages, it is more efficient to use the stem rather than the word as the core unit of abstraction. Our contributions are: 1) we propose an unsupervised stem-based cross-lingual approach for POS tagging for low-resource languages of rich morphology; 2) we further investigate morpheme-level alignment and projection; and 3) we examine whether the use of linguistic priors for morphological segmentation improves POS tagging. We conduct experiments using six source languages and eight morphologically complex target languages of diverse typologies. Our results show that the stem-based approach improves the POS models for all the target languages, with an average relative error reduction of 10.3% in accuracy per target language, and outperforms the word-based approach that operates on three-times more data for about two thirds of the language pairs we consider. Moreover, we show that morpheme-level alignment and projection and the use of linguistic priors for morphological segmentation further improve POS tagging. 
    more » « less
  4. ; ; ; ; ; (, Biophysical Reports)
    Magnetic resonance imaging (MRI) is a highly significant imaging platform for a variety of medical and research applications. However, the low spatiotemporal resolution of conventional MRI limits its applicability toward rapid acquisition of ultrahigh-resolution scans. Current aims at high-resolution MRI focus on increasing the accuracy of tissue delineation, as- sessments of structural integrity, and early identification of malignancies. Unfortunately, high-resolution imaging often leads to decreased signal/noise (SNR) and contrast/noise (CNR) ratios and increased time cost, which are unfeasible in many clinical and academic settings, offsetting any potential benefits. In this study, we apply and assess the efficacy of super-res- olution reconstruction (SRR) through iterative back-projection utilizing through-plane voxel offsets. SRR allows for high-res- olution imaging in condensed time frames. Rat skulls and archerfish samples, typical models in academic settings, were used to demonstrate the impact of SRR on varying sample sizes and applicability for translational and comparative neuroscience. The SNR and CNR increased in samples that did not fully occupy the imaging probe and in instances where the low-resolution data were acquired in three dimensions, while the CNR was found to increase with both 3D and 2D low-resolution data recon- structions when compared with directly acquired high-resolution images. Limitations to the applied SRR algorithm were inves- tigated to determine the maximum ratios between low-resolution inputs and high-resolution reconstructions and the overall cost effectivity of the strategy. Overall, the study revealed that SRR could be used to decrease image acquisition time, in- crease the CNR in nearly all instances, and increase the SNR in small samples. 
    more » « less
  5. ; (, Radio Science)
    Abstract We have recently introduced a modification of the multiple signal classification method for synthetic aperture radar. This method incorporates a user‐defined parameter,ϵ, that allows for tunable quantitative high‐resolution imaging. However, this method requires relatively large single‐to‐noise ratios (SNR) to work effectively. Here, we first identify the fundamental mechanism in that method that produces high‐resolution images. Then we introduce a modification to Kirchhoff Migration (KM) that uses the same mechanism to produce tunable, high‐resolution images. This modified KM method can be applied to low SNR measurements. We show simulation results that demonstrate the features of this method. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email