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Cryo-electron tomography : a journey from sample preparation to data mining /

"Cryo-Electron Tomography: A Journey from Sample Preparation to Data Mining providing a holistic overview of this rapidly advancing field and equipping researchers with the knowledge and tools necessary to initiate their own investigations. The book begins with a section on advanced cryogenic s...

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Bibliographic Details
Corporate Author: ScienceDirect (Online service)
Other Authors: Hanein, Dorit (Editor), Volkmann, Niels (Editor)
Format: eBook
Language:English
Published: Amsterdam : Academic Press, 2025.
Subjects:
Cryoelectronics.
Tomography.
Cryoélectronique.
Tomographie.
Cryoelectronics
Tomography
Electronic books.
Online Access:Connect to the full text of this electronic book
Table of Contents:
  • 1. Characteristics of sample preparation for electron microscopy / Seth A. Villarreal
  • 2. Cryo-FIB developments to enable nanoscale biopsies / Alexander Rigort and Andrew Leis
  • 3. Preparing bacterial cells for cryo-electron tomography / Mohammed Kaplan, William J. Nicolas and Grant J. Jensen
  • 4. Revealing the hidden world of microbes in situ: Sample preparation workflows for cryo-electron tomography / Samira Heydari and Jun Liu
  • 5. Mastering the preparation of eukaryotic cell samples for cryo-ET: Tips and techniques / Cécile Sauvanet and Dorit Hanein
  • 6. Interpretation of cellular tomograms / Niels Volkmann
  • 7. Denoising in cryoET / Jose-Jesus Fernandez
  • 8. Feature detection in cryo-electron tomography image analysis / Mostofa Rafid Uddin, Sajib Acharjee Dip, Rajat Aayush Jha, Xiangrui Zeng and Min Xu
  • 9. Validation methods in cryo-electron tomography / F.P. de Isidro-Gómez, J.L. Vilas, E. Fernández-Giménez, O.L. Zarrabeitia, D. Marchán, M. Iceta, D. Herreros, P. Conesa, Y.C. Fonseca, J. Jiménez de la Morena, A. Cuervo, P. Losana, C.O.S. Sorzano and J.M. Carazo.
  • 1
  • Characteristics of sample preparation for electron microscopy
  • Introduction
  • Methods of Imaging by Electron Microscopy
  • Sample stability
  • Cryofixation
  • Workflow comparisons
  • Conclusions
  • References
  • 2
  • Cryo-FIB developments to enable nanoscale biopsies
  • Introduction
  • The rise of cryo-FIB in structural biology
  • Micromachining cryo-lamellae
  • Technological advancements
  • Properties of plasma FIB beams
  • Assessing beam damage on cryo-lamellae
  • Toward more challenging samples
  • Another dimension
  • from 2D to 3D cell culture
  • Importance of correlative cryo-fluorescence microscopy
  • Bulk sample processing
  • Role of automation for in situ tomography
  • Streamlining cryo-lamella preparation
  • Outlook
  • Acknowledgments
  • References
  • 3
  • Preparing bacterial cells for cryo-electron tomography
  • Introduction
  • Sample preparation
  • Bacterial growth
  • Imaging individual cells
  • Imaging cell-cell interactions
  • Other tips
  • Preparing grids for cryo-ET
  • Gold fiducials
  • Freezing samples
  • Thinning samples
  • Collecting data
  • Analysis and data storage (and significance of cryo-ET database)
  • Concluding remarks
  • Acknowledgments
  • References
  • 4
  • Revealing the hidden world of microbes in situ: Sample preparation workflows for cryo-electron tomography
  • Introduction
  • An overview of the cryo-ET workflow
  • Sample preparation for direct cryo-ET imaging
  • Intact bacteria with thin diameter
  • Preparing bacterial culture
  • Collecting bacteria
  • Bacterial minicells
  • Bacteria-host interactions: Extracellular pathogens
  • Frozen-hydrated specimen preparation
  • Grid type and preparation.
  • Vitrification
  • Clipping
  • Sample preparation for cryo-FIB-ET imaging
  • Bacteria-host interactions: Intracellular pathogens
  • Grid preparation
  • Target localization
  • Cryo-FIB milling
  • Mapping
  • Milling
  • Summary and outlook
  • Acknowledgments
  • References
  • 5
  • Mastering the preparation of eukaryotic cell samples for cryo-ET: Tips and techniques
  • Summary
  • Preparation of cell-culture-amenable cryo-ET substrates
  • Grids
  • What size mesh, hole, and distribution?
  • Holey grids
  • Making grids cell culture compatible
  • Grids sterilization
  • Increasing efficient cell seeding
  • Seeding cells
  • Vitrification
  • Manual plunger versus automated (Vitrobot/EMGP)
  • Sample thickness
  • Prior to vitrification
  • Cryo-CLEM
  • Fiducials
  • Gold fiducial
  • Dual-purpose fluorescent fiducial
  • Cell integrity and sample quality assessment
  • Perspectives
  • Cell suspension
  • Grid functionalization
  • References
  • 6
  • Interpretation of cellular tomograms
  • Introduction
  • The need for holistic approaches to tomogram interpretation
  • Tomogram enhancements
  • Membrane segmentation
  • Tracing of filamentous structures
  • Analysis of cellular architecture
  • Outlook and conclusion
  • References
  • 7
  • Denoising in cryoET
  • Introduction
  • Basic concepts of filtering in the real and Fourier space
  • Handling noise during tomographic reconstruction
  • Denoising tomograms
  • Linear methods
  • Gaussian filter
  • Nonlinear methods
  • Median filter
  • Beltrami flow
  • Other nonlinear methods
  • Anisotropic methods
  • Bilateral filtering
  • Nonlocal means
  • Anisotropic nonlinear diffusion
  • Deep-learning approaches to denoising tomograms
  • Contrast improvement through CTF deconvolution
  • Software
  • Concluding remarks
  • Acknowledgments
  • References
  • 8
  • Feature detection in cryo-electron tomography image analysis
  • Introduction.
  • Feature enhancement
  • Denoising
  • Wavelet-based denoising methods
  • Neural-network-based denoising methods
  • Missing wedge compensation
  • MW compensation during reconstruction
  • MW compensation after reconstruction
  • Saliency detection
  • Feature object detection
  • Particle picking
  • Membrane-bounded particle detection
  • Ultrastructure detection
  • Feature semantic segmentation
  • Deep semantic segmentation of subtomograms
  • Membrane segmentation
  • Feature representation learning and classification
  • Subtomogram classification and clustering
  • Feature representation learning and pattern mining
  • Feature structural recovery
  • Subtomogram alignment and averaging
  • Continuous conformational variability analysis
  • Discussion and conclusion
  • References
  • 9
  • Validation methods in cryo-electron tomography
  • Introduction
  • The cryoET image processing workflow
  • Movie alignment
  • Validation methods
  • Tilt-series alignment
  • Validation methods
  • Contrast transfer function (CTF)
  • Validation methods
  • Tomogram reconstruction
  • Validation methods
  • Tomogram postprocessing
  • Proposed validation methods
  • Particle picking
  • Validation methods
  • Proposed validation methods
  • Subtomogram averaging: Alignment and classification
  • Validation methods
  • Quality of the average map
  • Validation methods
  • Workflow validation strategies
  • Validation methods
  • Emerging topics in cryoET validation
  • Acknowledgment
  • References
  • Index.