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

Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

8.7K
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...
8.7K
Super-resolution Fluorescence Microscopy01:37

Super-resolution Fluorescence Microscopy

12.1K
Super-resolution fluorescence microscopy (SRFM) provides a better resolution than conventional fluorescence microscopy by reducing the point spread function (PSF). PSF is the light intensity distribution from a point that causes it to appear blurred. Due to PSF, each fluorescing point appears bigger than its actual size, and it is the PSF interference of nearby fluorophores that causes the blurred image. Various approaches to achieving higher resolution through SRFM have recently been...
12.1K
Immunofluorescence Microscopy01:12

Immunofluorescence Microscopy

12.8K
A fluorescence microscope uses fluorescent chromophores called fluorochromes, which can absorb energy from a light source and then emit this energy as visible light. Fluorochromes include naturally fluorescent substances (such as chlorophylls) and fluorescent stains that are added to the specimen to create contrast. Dyes such as Texas red and FITC are examples of fluorochromes. Other examples include the nucleic acid dyes 4’,6’-diamidino-2-phenylindole (DAPI), and acridine orange.
12.8K
Phase Contrast and Differential Interference Contrast Microscopy01:26

Phase Contrast and Differential Interference Contrast Microscopy

11.9K
Phase-Contrast Microscopes
In-phase-contrast microscopes, interference between light directly passing through a cell and light refracted by cellular components is used to create high-contrast, high-resolution images without staining. It is the oldest and simplest type of microscope that creates an image by altering the wavelengths of light rays passing through the specimen. Altered wavelength paths are created using an annular stop in the condenser. The annular stop produces a hollow cone of...
11.9K
Confocal Fluorescence Microscopy01:16

Confocal Fluorescence Microscopy

19.8K
Confocal microscopy is an advanced microscopic technique. The prime advantage of the confocal microscope over other microscopy techniques is its ability to block the out-of-focus light from the illuminated samples using pinholes. It is widely used with fluorescence optics to obtain high-resolution, sharp contrast images. Unlike optical microscopes, confocal microscopes use a focused beam of light laser to scan the entire sample surface at different z-planes. These microscopes are, therefore,...
19.8K
X-ray Imaging01:24

X-ray Imaging

9.7K
German physicist Wilhelm Röntgen (1845–1923) was experimenting with electrical current when he discovered that a mysterious and invisible "ray" would pass through his flesh but leave an outline of his bones on a screen coated with a metal compound. In 1895, Röntgen made the first durable record of the internal parts of a living human: an "X-ray" image (as it came to be called) of his wife’s hand. Scientists worldwide quickly began their own experiments with...
9.7K

You might also read

Related Articles

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

Sort by
Same author

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same author

Systematic characterisation of site-specific proline hydroxylation using hydrophilic interaction chromatography and mass spectrometry.

eLife·2026
Same author

PHD1-dependent hydroxylation of RepoMan (CDCA2) on P604 modulates the control of mitotic progression.

eLife·2026
Same author

Search, organize, aggregate and share image data with BioFile Finder (BFF).

Nature methods·2026
Same author

Exploring the Continuing Education Experiences and Needs of Hearing Health Care Professionals: A Survey-Based Study.

American journal of audiology·2026
Same author

Pediatric Intensive Care-Associated Parental Traumatic Stressors by Parent Report: Beyond the First Year.

Journal of patient experience·2026
See all related articles

Related Experiment Video

Updated: Jan 6, 2026

Computer-assisted Large-scale Visualization and Quantification of Pancreatic Islet Mass, Size Distribution and Architecture
16:59

Computer-assisted Large-scale Visualization and Quantification of Pancreatic Islet Mass, Size Distribution and Architecture

Published on: March 4, 2011

12.7K

Bringing Open Data to Whole Slide Imaging.

Sébastien Besson1, Roger Leigh1, Melissa Linkert2

  • 1Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.

Digital Pathology : 15Th European Congress, ECDP 2019, Warwick, UK, April 10-13, 2019 : Proceedings. European Congress on Digital Pathology (15Th : 2019 : Warwick, England)
|October 4, 2019
PubMed
Summary
This summary is machine-generated.

Digital pathology faces challenges with whole slide imaging (WSI) file formats. Researchers extended the OME-TIFF format to efficiently store multi-resolution WSI data, improving digital pathology workflows.

Keywords:
OME-TIFFopen dataopen file formatwhole slide imaging

More Related Videos

Automated Slide Scanning and Segmentation in Fluorescently-labeled Tissues Using a Widefield High-content Analysis System
09:33

Automated Slide Scanning and Segmentation in Fluorescently-labeled Tissues Using a Widefield High-content Analysis System

Published on: May 3, 2018

8.4K
Introduction of an Integrated Pathology Image Management, Artificial Intelligence, and Reporting System
05:33

Introduction of an Integrated Pathology Image Management, Artificial Intelligence, and Reporting System

Published on: July 11, 2025

738

Related Experiment Videos

Last Updated: Jan 6, 2026

Computer-assisted Large-scale Visualization and Quantification of Pancreatic Islet Mass, Size Distribution and Architecture
16:59

Computer-assisted Large-scale Visualization and Quantification of Pancreatic Islet Mass, Size Distribution and Architecture

Published on: March 4, 2011

12.7K
Automated Slide Scanning and Segmentation in Fluorescently-labeled Tissues Using a Widefield High-content Analysis System
09:33

Automated Slide Scanning and Segmentation in Fluorescently-labeled Tissues Using a Widefield High-content Analysis System

Published on: May 3, 2018

8.4K
Introduction of an Integrated Pathology Image Management, Artificial Intelligence, and Reporting System
05:33

Introduction of an Integrated Pathology Image Management, Artificial Intelligence, and Reporting System

Published on: July 11, 2025

738

Area of Science:

  • Digital Pathology
  • Bioimaging
  • Computational Pathology

Background:

  • The increasing volume of digital pathology data necessitates robust file formats.
  • Existing whole slide imaging (WSI) formats present challenges in managing multi-resolution data.
  • The Open Microscopy Environment Tagged Image File Format (OME-TIFF) is a widely adopted standard.

Purpose of the Study:

  • To extend the OME-TIFF format for efficient storage of multi-resolution whole slide images.
  • To describe the structural enhancements and performance characteristics of the modified OME-TIFF format.
  • To introduce open-source library support for reading and writing these enhanced OME-TIFF files.

Main Methods:

  • Leveraging the core TIFF specification to incorporate multi-resolution (pyramidal) image data.
  • Implementing flexible and performant data storage strategies within the OME-TIFF structure.
  • Developing and validating open-source software for OME-TIFF creation and access.

Main Results:

  • Demonstrated the successful extension of OME-TIFF to accommodate pyramidal WSI data.
  • Characterized the performance benefits of the new format for digital pathology applications.
  • Provided accessible open-source tools for widespread adoption.

Conclusions:

  • The extended OME-TIFF format offers a flexible and performant solution for managing whole slide imaging data.
  • This advancement supports the growing needs of digital pathology and bioimaging research.
  • Open-source library support facilitates the integration and utilization of this improved file format.