Related Experiment Video
Updated: Jun 6, 2025

Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions
Published on: June 24, 2013
CELS-3D-Cutting edge light source for exciting fluorescence in microtome-based 3D microscopy and targeted correlative
Vladyslav Denyshchenko1, Christopher Evans2, Tiina O'Neill1
1Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
A novel light sheet illumination method uses an ultramicrotome knife to enable 3D imaging of large, opaque samples. This Cutting Edge Light Source, Three-Dimensional (CELS-3D) system allows for detailed reconstruction of structures previously inaccessible to confocal microscopy.
Area of Science:
- Microscopy and Imaging Technologies
- Biotechnology
- Materials Science
Background:
- Traditional microscopy techniques struggle with imaging large, non-transparent biological samples due to light penetration limitations.
- Confocal microscopy, for instance, can only image depths up to 50 μm in dense samples like liver spheroids.
- There is a need for advanced imaging methods capable of deep tissue visualization and targeted feature identification.
Purpose of the Study:
- To introduce a novel imaging system, CELS-3D (Cutting Edge Light Source, Three-Dimensional), for 3D imaging of biological samples.
- To demonstrate the utility of CELS-3D for deep imaging of large, non-transparent specimens, overcoming limitations of existing technologies.
- To showcase CELS-3D's capability for targeted correlative microscopy by visualizing fluorescence during serial sectioning.
Main Methods:
- Developed a prototype microscope (CELS-3D) that utilizes light exiting an ultramicrotome's glass knife as an oblique light sheet for sample illumination.
- Mounted the CELS-3D system on an ultramicrotome for serial sectioning and 3D imaging of biological samples.
- Characterized the CELS-3D system and applied it to 3D imaging of human liver spheroids and targeted correlative microscopy of C. elegans.
Main Results:
- Successfully achieved 3D imaging and reconstruction of nuclei and tight junctions throughout 500 μm human liver spheroids.
- Demonstrated that CELS-3D can image samples to depths far exceeding the capabilities of confocal microscopy.
- Successfully applied CELS-3D for targeted correlative microscopy of human liver spheroids and C. elegans, identifying fluorescent features during sectioning.
Conclusions:
- CELS-3D provides a breakthrough in 3D imaging of less- and non-transparent samples, including organoids, biopsies, cartilage, and bone.
- The system's ability to provide online fluorescence visualization during sectioning facilitates targeted correlative microscopy.
- CELS-3D is easily mountable on commercial ultramicrotomes and offers an intuitive operation for advanced biological imaging.
Related Concept Videos
Three-Dimensional Microscopy in Microbiology
Confocal Fluorescence Microscopy
Super-resolution Fluorescence Microscopy

