Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

4.1K
Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
4.1K
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

2.8K
Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
2.8K
Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

8.8K
Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...
8.8K
Transmission Electron Microscopy01:15

Transmission Electron Microscopy

6.8K
In 1931, physicist Ernst Ruska—building on the idea that magnetic fields can direct an electron beam just as lenses can direct a beam of light in an optical microscope—developed the first prototype of the electron microscope. This development led to the development of the field of electron microscopy. In the transmission electron microscope (TEM), electrons are produced by a hot tungsten element and accelerated by a potential difference in an electron gun, which gives them up to 400...
6.8K
Preparation of Samples for Electron Microscopy01:20

Preparation of Samples for Electron Microscopy

6.7K
To be visualized by an electron microscope, either transmission or scanning, biological samples need to be fixed (stabilized) so the electron beam does not destroy them and dried thoroughly (desiccated/dehydrated) so the vacuum does not affect them. Fixation needs to be done as quickly as possible because the sample properties will start changing as soon as it is removed from its natural environment. For example, in a tissue sample, the oxygen levels begin decreasing, causing an altered...
6.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A pico-calorimeter for cellular metabolism and antimicrobial susceptibility testing.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

<i>seekrflow</i>: Towards an End-to-End Automated Simulation Pipeline with Machine-Learned Force Fields for Accelerated Drug-Target Kinetic and Thermodynamic Predictions.

Journal of chemical theory and computation·2026
Same author

Cryo-Electron Microscopy Structural Ensemble Optimization Using Individual Particles.

Journal of chemical theory and computation·2026
Same author

Study of Protein-Protein Interactions in Septin Assembly: Multiple amphipathic helix domains cooperate in binding to the lipid membrane.

PLoS computational biology·2026
Same author

Counting particles in cryo-electron microscopy may result in incorrect population estimates.

Communications biology·2026
Same author

Machine learning for biomolecular modeling.

The Journal of chemical physics·2026
Same journal

Layered social competition coordinates reproductive hierarchy formation in ants.

bioRxiv : the preprint server for biology·2026
Same journal

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas.

bioRxiv : the preprint server for biology·2026
Same journal

Loss of LanC-like proteins delays post-injury regeneration of aging skeletal muscles.

bioRxiv : the preprint server for biology·2026
Same journal

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets.

bioRxiv : the preprint server for biology·2026
Same journal

Confidence-supported label-free metabolic imaging with FPhaS phase autofluorescence microscopy.

bioRxiv : the preprint server for biology·2026
Same journal

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Jan 10, 2026

Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells
11:55

Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells

Published on: May 28, 2021

4.6K

cryoJAX: A Cryo-electron Microscopy Image Simulation Library In JAX.

Michael J O'Brien1, David Silva-Sánchez2, Geoffrey Woollard3

  • 1Department of Physics, Harvard University, Cambridge, 02143, MA, USA.

Biorxiv : the Preprint Server for Biology
|November 24, 2025
PubMed
Summary
This summary is machine-generated.

Cryo-electron microscopy (cryo-EM) is expanding beyond molecular complexes to study cellular organization. The new cryoJAX library, built on JAX, offers a flexible framework for computationally intensive cryo-EM data analysis.

Keywords:
automatic differentiationbiophysicscryo-EMimage simulationsoftware library

More Related Videos

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction
09:25

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

Published on: January 9, 2015

46.9K
A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion
13:43

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

14.9K

Related Experiment Videos

Last Updated: Jan 10, 2026

Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells
11:55

Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells

Published on: May 28, 2021

4.6K
Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction
09:25

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

Published on: January 9, 2015

46.9K
A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion
13:43

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

14.9K

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Cryo-electron microscopy (cryo-EM) excels at atomic resolution imaging of biomolecular complexes.
  • Emerging applications of cryo-EM include investigating intracellular organization and heterogeneous molecular states.
  • Analyzing cryo-EM data for these advanced applications presents significant computational challenges.

Purpose of the Study:

  • To address the computational demands of advanced cryo-EM data analysis.
  • To develop a flexible and efficient computational framework for cryo-EM image simulation and analysis.
  • To leverage the JAX scientific computing framework for cryo-EM data processing.

Main Methods:

  • Development of cryoJAX, a cryo-EM image simulation library within the JAX ecosystem.
  • Utilizing JAX's capabilities for automatic differentiation and vectorization.
  • Creating a flexible modeling language for cryo-EM image formation.

Main Results:

  • CryoJAX provides a robust platform for building computational cryo-EM data analysis tools.
  • The library supports a wide range of downstream data analysis applications.
  • Integration with JAX facilitates the development and deployment of novel cryo-EM algorithms.

Conclusions:

  • CryoJAX enhances the utility of cryo-EM for complex biological investigations beyond molecular structures.
  • The JAX-based framework accelerates the development of advanced cryo-EM data analysis methods.
  • CryoJAX is poised to support the growing breadth of scientific applications for cryo-EM.