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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...

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Updated: Jun 25, 2026

A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery

A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery

Published on: May 20, 2016

Appion: an integrated, database-driven pipeline to facilitate EM image processing.

Gabriel C Lander¹, Scott M Stagg, Neil R Voss

¹National Resource for Automated Molecular Microscopy, The Scripps Research Institute, CB 129, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA.

Journal of Structural Biology

|March 6, 2009

Summary

This summary is machine-generated.

Appion provides a transparent and manageable pipeline for cryo-electron microscopy (cryo-EM) data processing. This system simplifies raw data to 3D reconstruction, enhancing user accessibility and result interpretation.

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Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Cryo-electron microscopy (cryo-EM) and 3D image reconstruction are increasingly vital in structural biology.
Existing cryo-EM workflows can be complex, posing challenges for data management and result interpretation.

Purpose of the Study:

To develop a transparent and user-friendly pipeline for cryo-EM data processing.
To facilitate the workflow from raw data to reliable 3D reconstructions.
To improve the accessibility of cryo-EM analysis for users with varying expertise.

Main Methods:

Appion, a modular and transparent pipeline integrated with a SQL database.
Web-based forms for user control of software modules.
Web-based viewers for transparent visualization of results linked to the database.
An extensible API designed for broad specimen compatibility.

Main Results:

A working prototype of the Appion pipeline has been developed and tested.
The pipeline successfully manages processing steps and enhances result transparency.
Naive users can efficiently assess the quality of their cryo-EM reconstructions.

Conclusions:

Appion offers a streamlined and accessible approach to cryo-EM data analysis.
The pipeline's modular design and transparent results improve the efficiency and reliability of 3D image reconstruction.
Appion empowers users to achieve high-quality cryo-EM results with greater ease.