biblio.bib

@article{eisenstein_2019,
	title = {Improved applicability and robustness of fast cryo-electron tomography data acquisition},
	volume = {208},
	issn = {1047-8477},
	url = {http://www.sciencedirect.com/science/article/pii/S1047847719301765},
	doi = {10.1016/j.jsb.2019.08.006},
	abstract = {The power of cryo-electron tomography (cryoET) lies in its capability to characterize macromolecules in their cellular context. Structure determination by cryoET, however, is time-consuming compared to single particle approaches. A recent study reported significant acceleration of data acquisition by a fast-incremental single-exposure (FISE) tilt series scheme. Here we improved the method and evaluated its efficiency and performance. We show that (1) FISE combined with the latest generation of direct electron detectors speeds up collection considerably, (2) previous generation (pre-2017) double-tilt axis Titan Krios holders are also suitable for FISE data acquisition, (3) x, y and z-specimen shifts can be compensated for, and (4) FISE tilt series data can generate averages of sub-nanometer resolution. These advances will allow for a widespread adoption of cryoET for high-throughput in situ studies and high-resolution structure determination across different biological research disciplines.},
	language = {en},
	number = {2},
	urldate = {2020-02-27},
	journal = {Journal of Structural Biology},
	author = {Eisenstein, Fabian and Danev, Radostin and Pilhofer, Martin},
	month = nov,
	year = {2019},
	keywords = {Calibration, Cryo-electron tomography, Cryo-EM, Data acquisition, Electron cryotomography, K2, K3, Throughput, Tilt series},
	pages = {107--114},
	file = {ScienceDirect Snapshot:/home/tom/Zotero/storage/8G7WG5RZ/S1047847719301765.html:text/html;ScienceDirect Full Text PDF:/home/tom/Zotero/storage/MQHVFK9D/Eisenstein et al. - 2019 - Improved applicability and robustness of fast cryo.pdf:application/pdf}
}

@article{volume_normalized_SPW,
	title = {Optimal noise reduction in {3D} reconstructions of single particles using a volume-normalized filter},
	volume = {180},
	issn = {1047-8477},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498508/},
	doi = {10.1016/j.jsb.2012.05.005},
	abstract = {The high noise level found in single-particle electron cryo-microscopy (cryo-EM) image data presents a special challenge for three-dimensional (3D) reconstruction of the imaged molecules. The spectral signal-to-noise ratio (SSNR) and related Fourier shell correlation (FSC) functions are commonly used to assess and mitigate the noise-generated error in the reconstruction. Calculation of the SSNR and FSC usually includes the noise in the solvent region surrounding the particle and therefore does not accurately reflect the signal in the particle density itself. Here we show that the SSNR in a reconstructed 3D particle map is linearly proportional to the fractional volume occupied by the particle. Using this relationship, we devise a novel filter (the “single-particle Wiener filter”) to minimize the error in a reconstructed particle map, if the particle volume is known. Moreover, we show how to approximate this filter even when the volume of the particle is not known, by optimizing the signal within a representative interior region of the particle. We show that the new filter improves on previously proposed error-reduction schemes, including the conventional Wiener filter as well as figure-of-merit weighting, and quantify the relationship between all of these methods by theoretical analysis as well as numeric evaluation of both simulated and experimentally collected data. The single-particle Wiener filter is applicable across a broad range of existing 3D reconstruction techniques, but is particularly well suited to the Fourier inversion method, leading to an efficient and accurate implementation.},
	number = {1},
	urldate = {2020-03-26},
	journal = {Journal of structural biology},
	author = {Sindelar, Charles V. and Grigorieff, Nikolaus},
	month = oct,
	year = {2012},
	pmid = {22613568},
	pmcid = {PMC3498508},
	pages = {26--38},
	file = {PubMed Central Full Text PDF:/home/tom/Zotero/storage/VJPJJUQH/Sindelar and Grigorieff - 2012 - Optimal noise reduction in 3D reconstructions of s.pdf:application/pdf}
}


@article{bharat_2015,
	title = {Advances in {Single}-{Particle} {Electron} {Cryomicroscopy} {Structure} {Determination} applied to {Sub}-tomogram {Averaging}},
	volume = {23},
	issn = {0969-2126},
	url = {http://www.sciencedirect.com/science/article/pii/S0969212615002798},
	doi = {10.1016/j.str.2015.06.026},
	abstract = {Recent innovations in specimen preparation, data collection, and image processing have led to improved structure determination using single-particle electron cryomicroscopy (cryo-EM). Here we explore some of these advances to improve structures determined using electron cryotomography (cryo-ET) and sub-tomogram averaging. We implement a new three-dimensional model for the contrast transfer function, and use this in a regularized likelihood optimization algorithm as implemented in the RELION program. Using direct electron detector data, we apply both single-particle analysis and sub-tomogram averaging to analyze radiation-induced movements of the specimen. As in single-particle cryo-EM, we find that significant sample movements occur during tomographic data acquisition, and that these movements are substantially reduced through the use of ultrastable gold substrates. We obtain a sub-nanometer resolution structure of the hepatitis B capsid, and show that reducing radiation-induced specimen movement may be central to attempts at further improving tomogram quality and resolution.},
	language = {en},
	number = {9},
	urldate = {2020-03-26},
	journal = {Structure},
	author = {Bharat, Tanmay A. M. and Russo, Christopher J. and L\"{o}we, Jan and Passmore, Lori A. and Scheres, Sjors H. W.},
	month = sep,
	year = {2015},
	pages = {1743--1753},
	file = {ScienceDirect Snapshot:/home/tom/Zotero/storage/AVRK2PKK/S0969212615002798.html:text/html;ScienceDirect Full Text PDF:/home/tom/Zotero/storage/WJCDD9WA/Bharat et al. - 2015 - Advances in Single-Particle Electron Cryomicroscop.pdf:application/pdf}
}


@article{rosenthal_2003,
	title = {Optimal {Determination} of {Particle} {Orientation}, {Absolute} {Hand}, and {Contrast} {Loss} in {Single}-particle {Electron} {Cryomicroscopy}},
	volume = {333},
	issn = {0022-2836},
	url = {http://www.sciencedirect.com/science/article/pii/S0022283603010222},
	doi = {10.1016/j.jmb.2003.07.013},
	abstract = {A computational procedure is described for assigning the absolute hand of the structure of a protein or assembly determined by single-particle electron microscopy. The procedure requires a pair of micrographs of the same particle field recorded at two tilt angles of a single tilt-axis specimen holder together with the three-dimensional map whose hand is being determined. For orientations determined from particles on one micrograph using the map, the agreement (average phase residual) between particle images on the second micrograph and map projections is determined for all possible choices of tilt angle and axis. Whether the agreement is better at the known tilt angle and axis of the microscope or its inverse indicates whether the map is of correct or incorrect hand. An increased discrimination of correct from incorrect hand (free hand difference), as well as accurate identification of the known values for the tilt angle and axis, can be used as targets for rapidly optimizing the search or refinement procedures used to determine particle orientations. Optimized refinement reduces the tendency for the model to match noise in a single image, thus improving the accuracy of the orientation determination and therefore the quality of the resulting map. The hand determination and refinement optimization procedure is applied to image pairs of the dihydrolipoyl acetyltransferase (E2) catalytic core of the pyruvate dehydrogenase complex from Bacillus stearothermophilus taken by low-dose electron cryomicroscopy. Structure factor amplitudes of a three-dimensional map of the E2 catalytic core obtained by averaging untilted images of 3667 icosahedral particles are compared to a scattering reference using a Guinier plot. A noise-dependent structure factor weight is derived and used in conjunction with a temperature factor (B=−1000\r{A}2) to restore high-resolution contrast without amplifying noise and to visualize molecular features to 8.7\r{A} resolution, according to a new objective criterion for resolution assessment proposed here.},
	language = {en},
	number = {4},
	urldate = {2020-03-26},
	journal = {Journal of Molecular Biology},
	author = {Rosenthal, Peter B. and Henderson, Richard},
	month = oct,
	year = {2003},
	keywords = {absolute hand, electron cryomicroscopy, pyruvate dehydrogenase, single particle reconstruction, tilt pairs},
	pages = {721--745},
	file = {ScienceDirect Snapshot:/home/tom/Zotero/storage/4PMZHT8J/S0022283603010222.html:text/html;ScienceDirect Full Text PDF:/home/tom/Zotero/storage/6QLELFJU/Rosenthal and Henderson - 2003 - Optimal Determination of Particle Orientation, Abs.pdf:application/pdf}
}


@article {exposure_grant_2015,
article_type = {journal},
title = {Measuring the optimal exposure for single particle cryo-EM using a 2.6 \angstrom reconstruction of rotavirus VP6},
author = {Grant, Timothy and Grigorieff, Nikolaus},
editor = {Sundquist, Wesley I},
volume = 4,
year = 2015,
month = {may},
pub_date = {2015-05-29},
pages = {e06980},
citation = {eLife 2015;4:e06980},
doi = {10.7554/eLife.06980},
url = {https://doi.org/10.7554/eLife.06980},
abstract = {Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 Å resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/Å\textsuperscript{2}, we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions, our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This ‘high-exposure’ technique should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass.},
keywords = {high-dose imaging, movie processing, radiation damage, optimal exposure, 20S proteasome, tomography},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}

@article{conical_fsc,
title = "Conical Fourier shell correlation applied to electron tomograms",
journal = "Journal of Structural Biology",
volume = "190",
number = "2",
pages = "215 - 223",
year = "2015",
issn = "1047-8477",
doi = "https://doi.org/10.1016/j.jsb.2015.03.010",
url = "http://www.sciencedirect.com/science/article/pii/S1047847715000726",
author = "C.A. Diebolder and F.G.A. Faas and A.J. Koster and R.I. Koning",
keywords = "Cryo-electron microscopy, Resolution estimation, Dual-axis cryo-electron tomography, Fourier shell correlation, Conical Fourier shell correlation",
abstract = "The resolution of electron tomograms is anisotropic due to geometrical constraints during data collection, such as the limited tilt range and single axis tilt series acquisition. Acquisition of dual axis tilt series can decrease these effects. However, in cryo-electron tomography, to limit the electron radiation damage that occurs during imaging, the total dose should not increase and must be fractionated over the two tilt series. Here we set out to determine whether it is beneficial fractionate electron dose for recording dual axis cryo electron tilt series or whether it is better to perform single axis acquisition. To assess the quality of tomographic reconstructions in different directions here we introduce conical Fourier shell correlation (cFSCe/o). Employing cFSCe/o, we compared the resolution isotropy of single-axis and dual-axis (cryo-)electron tomograms using even/odd split data sets. We show that the resolution of dual-axis simulated and cryo-electron tomograms in the plane orthogonal to the electron beam becomes more isotropic compared to single-axis tomograms and high resolution peaks along the tilt axis disappear. cFSCe/o also allowed us to compare different methods for the alignment of dual-axis tomograms. We show that different tomographic reconstruction programs produce different anisotropic resolution in dual axis tomograms. We anticipate that cFSCe/o can also be useful for comparisons of acquisition and reconstruction parameters, and different hardware implementations."
}

@article{fsc_mvh,
title = "Fourier shell correlation threshold criteria",
journal = "Journal of Structural Biology",
volume = "151",
number = "3",
pages = "250 - 262",
year = "2005",
issn = "1047-8477",
doi = "https://doi.org/10.1016/j.jsb.2005.05.009",
url = "http://www.sciencedirect.com/science/article/pii/S1047847705001292",
author = "Marin van Heel and Michael Schatz",
keywords = "Fourier shell correlation, Resolution criteria, Single particles, cryo-EM, Information",
abstract = "The resolution value claimed for an electron microscopical three-dimensional reconstruction indicates the overall quality of the experiment. The Fourier shell correlation (FSC) criterion has now become the standard quality measure. However, what has continued to be controversial is the issue of the FSC threshold level at which one defines the reproducible resolution. Here, we discuss the theoretical behaviour of the FSC in conjunction with the various factors which influence it: the number of “voxels” in a given Fourier shell, the symmetry of the structure, and the size of the structure within the reconstruction volume. Both the theoretical considerations and our model experiments show that fixed-valued FSC threshold (like “0.5”) may never be used in a reproducible criterion. Fixed threshold values are—as we show here—simply the result of incorrect assumptions in the basic statistics. Two families of FSC threshold curves are discussed: the σ-factor curves and the new family of bit-based information threshold curves. Whereas σ-factor curves indicate the resolution level at which one has collected information significantly above the noise level, the information curves indicate the resolution level at which enough information has been collected for interpretation."
}


@article{novaCTF,
	title = {Efficient {3D}-{CTF} correction for cryo-electron tomography using {NovaCTF} improves subtomogram averaging resolution to 3.4\r{A}},
	volume = {199},
	issn = {1095-8657},
	doi = {10.1016/j.jsb.2017.07.007},
	abstract = {Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4A resolution structure determined by subtomogram averaging.},
	language = {eng},
	number = {3},
	journal = {Journal of Structural Biology},
	author = {Turo\v{n}ov\'{a}, Beata and Schur, Florian K. M. and Wan, William and Briggs, John A. G.},
	year = {2017},
	pmid = {28743638},
	pmcid = {PMC5614107},
	keywords = {Capsid Proteins, Contrast transfer function, Cryo-electron microscopy, Cryoelectron Microscopy, Defocus, HIV-1, Image Processing, Computer-Assisted, Reconstruction, Reproducibility of Results, Software, Subtomogram averaging, Tomography, Weighted back projection, Workflow},
	pages = {187--195},
	file = {Full Text:/home/tom/Zotero/storage/6QZRJ6BM/Turoňová et al. - 2017 - Efficient 3D-CTF correction for cryo-electron tomo.pdf:application/pdf}
}

@article{jensen_3dctf,
title = "Defocus-gradient corrected back-projection",
journal = "Ultramicroscopy",
volume = "84",
number = "1",
pages = "57 - 64",
year = "2000",
issn = "0304-3991",
doi = "https://doi.org/10.1016/S0304-3991(00)00005-X",
url = "http://www.sciencedirect.com/science/article/pii/S030439910000005X",
author = "Grant J Jensen and Roger D Kornberg",
keywords = "Data processing, Image processing, Three-dimensional reconstruction",
abstract = "Three-dimensional reconstructions of icosahedral viruses from cryoelectron microscope images have reached resolutions where the microscope depth of field is a significant resolution-limiting factor. An analytical treatment presented here shows how the depth of field limitation can be understood as an envelope function which gradually attenuates the signal, starting well before the numerical depth of field is actually reached. A simple modification to the well-known back-projection reconstruction algorithm is described, called the defocus-gradient corrected back-projection, which computationally corrects for the contrast transfer function along a defocus gradient. Computer simulations demonstrate how the algorithm effectively eliminates the depth of field limitation."
}

@article{ccc_forster,
title = "Classification of cryo-electron sub-tomograms using constrained correlation",
journal = "Journal of Structural Biology",
volume = "161",
number = "3",
pages = "276 - 286",
year = "2008",
note = "The 4th International Conference on Electron Tomography",
issn = "1047-8477",
doi = "https://doi.org/10.1016/j.jsb.2007.07.006",
url = "http://www.sciencedirect.com/science/article/pii/S1047847707001566",
author = {Friedrich F\"{o}rster and Sabine Pruggnaller and Anja Seybert and Achilleas S. Frangakis},
keywords = "Electron tomography, Classification, Correlation, Multivariate statistical analysis, -Means",
abstract = "Cryo-electron tomography (CET) is currently the only three-dimensional imaging technique capable of visualizing macromolecules in their cellular context at close-to-native conditions with a resolution in the nanometer range. An important component for the analysis of the data is their classification, which should discriminate among various macromolecules, conformational changes and interaction partners. Missing structure factors, typically in a wedge-shaped region in Fourier space if single-axis tilting is performed, hamper classification of cryo-electron tomographic data. Here, we describe a classification method for three-dimensional (3D) sub-tomograms extracted from cryo-electron tomograms, which takes the missing wedge into account and provides reliable results. The similarity of the individually aligned sub-tomograms is scored by constrained correlation. Subsequently, they are clustered based on their pairwise correlation values. In order to demonstrate the feasibility of this approach, we apply the proposed method to simulated tomographic data of the chaperone thermosome in different conformations. By comparison of the principal components of the resulting matrix we show that the proposed metric is significantly less prone to the orientation of the missing wedge compared to the unconstrained correlation. Moreover, we apply our classification method to an experimental dataset of GroEL with and without GroES, where we achieve a distinct discrimination between the putative GroEL and GroEL/GroES complexes."
}

@article {Tegunov2020,
	author = {Tegunov, Dimitry and Xue, Liang and Dienemann, Christian and Cramer, Patrick and Mahamid, Julia},
	title = {Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.7\r{A} inside cells},
	elocation-id = {2020.06.05.136341},
	year = {2020},
	doi = {10.1101/2020.06.05.136341},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and in situ. In addition to aligning individual particles, accurate registration of sample motion and 3D deformation during exposures is crucial for achieving high resolution. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and improves the results of structure determination. M provides a unified optimization framework for both in vitro frame series and in situ tomographic tilt series data. We show that tilt series data can provide the same resolution as frame series, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M improves upon previous methods, and resolves a 70S ribosome bound to an antibiotic inside bacterial cells at a nominal resolution of 3.7 {\r A}. Thus, computational tools are now available to resolve structures from tomographic in situ cryo-EM data at residue level.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2020/06/05/2020.06.05.136341},
	eprint = {https://www.biorxiv.org/content/early/2020/06/05/2020.06.05.136341.full.pdf},
	journal = {bioRxiv}
}

@article{MASTRONARDE2017102,
title = "Automated tilt series alignment and tomographic reconstruction in IMOD",
journal = "Journal of Structural Biology",
volume = "197",
number = "2",
pages = "102 - 113",
year = "2017",
note = "Electron Tomography",
issn = "1047-8477",
doi = "https://doi.org/10.1016/j.jsb.2016.07.011",
url = "http://www.sciencedirect.com/science/article/pii/S1047847716301526",
author = "David N. Mastronarde and Susannah R. Held",
keywords = "Electron tomography, Tilt series alignment, Tomographic reconstruction, Automated processing",
abstract = "Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20\% improvement in alignment error for plastic-embedded samples and 10\% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention."
}