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Imaging Biological Samples with Optical Microscopy

Imaging Biological Samples with Optical Microscopy

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...

Scanning Electron Microscopy

Scanning Electron Microscopy

A scanning electron microscope (SEM) is used to study the surface features of a sample by using an electron beam that scans the sample surface in a two-dimensional manner. Typically, areas between ~1 centimeter to 5 micrometers in width can be imaged. SEM can be used to image bacteria, viruses, tissues as well as larger samples like insects. Conventional SEM gives a magnification ranging from 20X to 30,000X and spatial resolution of 50 to 100 nanometers.
Fundamental Principles
Accelerated...

X-ray Imaging

X-ray Imaging

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 X-rays, and by 1900, X-ray was widely...

Immunocytochemistry and Immunohistochemistry

Immunocytochemistry and Immunohistochemistry

Immunocytochemistry (ICC) and immunohistochemistry (IHC) are techniques that use antibodies to check for specific proteins or antigens in a sample. The technique was first published by Albert Coons in 1941 to detect the presence of pneumococcal antigen in tissue sections from mice infected with Pneumococcus. Immunocytochemistry helps localization of proteins or antigens in individual cells like blood cells, stem cells, etc., while immunohistochemistry does the same for tissue samples.
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Super-resolution Fluorescence Microscopy

Super-resolution Fluorescence Microscopy

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 developed.

Immunofluorescence Microscopy

Immunofluorescence Microscopy

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.
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Related Experiment Video

Updated: Jun 21, 2026

Hybrid µCT-FMT imaging and image analysis

Hybrid µCT-FMT imaging and image analysis

Published on: June 4, 2015

Content-based image retrieval for scientific literature access.

T M Deserno¹, S Antani, L Rodney Long

¹Department of Medical Informatics, Aachen University of Technology (RWTH), Aachen, Germany. deserno@ieee.org

Methods of Information in Medicine

|July 22, 2009

Summary

Content-based image retrieval (CBIR) can significantly improve access to scientific articles by searching figures. This method offers a predicted accuracy of 97.08% for article retrieval, enhancing medical literature search.

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Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases

Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases

Published on: October 24, 2019

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Last Updated: Jun 21, 2026

Hybrid µCT-FMT imaging and image analysis

Hybrid µCT-FMT imaging and image analysis

Published on: June 4, 2015

Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases

Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases

Published on: October 24, 2019

Area of Science:

Medical Informatics
Digital Libraries
Scientific Publishing

Background:

Traditional scientific literature access relies on text-based searches (title, author, abstract).
This alphanumeric search often overlooks valuable information contained within article figures.
Electronic publishing increases the volume of accessible scientific content.

Purpose of the Study:

To estimate the benefits of content-based image retrieval (CBIR) for accessing scientific articles.
To augment traditional text-based search methods with figure analysis.
To assess the impact of CBIR on medical literature retrieval.

Main Methods:

Selected four high-impact journals from JCR 2005.
Automatically extracted figures from PDF article files.
Quantitatively estimated retrieval accuracy using ImageCLEF data and validated qualitatively with IRMA project.

Main Results:

Analyzed 2077 articles, comprising 11,753 pages and 4493 figures (11,238 individual images).
Predicted article retrieval accuracy using CBIR reached 97.08%.
Demonstrated the potential of image retrieval in medical applications.

Conclusions:

Content-based image retrieval (CBIR) shows high potential for enhancing medical literature search.
CBIR offers a significant improvement over traditional alphanumeric search methods.
This technology can improve discoverability and access to scientific information within figures.