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Updated: Sep 29, 2025

Array Tomography Workflow for the Targeted Acquisition of Volume Information using Scanning Electron Microscopy
Published on: July 15, 2021
Correlative volume-imaging using combined array tomography and FIB-SEM tomography with beam deceleration for 3D
Shingo Hirashima1,2, Keisuke Ohta1,3, Yukiko Rikimaru-Nishi1,4
1Department of Anatomy, Division of Microscopic and Developmental Anatomy, Kurume University School of Medicine, Kurume 830-0011, Japan.
Focused ion beam scanning electron microscopy (FIB-SEM) challenges were overcome by combining array tomography and FIB-SEM tomography. This novel method reveals fine chondrocyte ultrastructure and dendritic processes for mesoscopic analysis.
Area of Science:
- Cell Biology
- Microscopy Techniques
- Biophysics
Background:
- Focused ion beam scanning electron microscopy (FIB-SEM) offers high spatial resolution for volume imaging.
- Analyzing deep biological structures with FIB-SEM is challenging due to limitations in imaging depth and sample preparation.
- Existing methods struggle to provide certainty in selecting analysis areas within resin-embedded samples.
Purpose of the Study:
- To develop a novel volume-imaging method combining array tomography and FIB-SEM tomography.
- To investigate the ultrastructure of chondrocytes, including fine surface details.
- To overcome the limitations of traditional FIB-SEM for analyzing deep biological structures.
Main Methods:
- Integration of array tomography with FIB-SEM tomography for enhanced imaging capabilities.
- Development of a method to precisely determine the analysis area, avoiding defects like cracks or poor staining.
- Application of the combined technique to study chondrocyte ultrastructure.
Main Results:
- The novel method successfully imaged chondrocyte ultrastructure with high fidelity.
- Fine dendritic processes on the chondrocyte surface, thinner than ultrathin sections, were visualized.
- The technique provides certainty in selecting analysis areas, improving reliability.
Conclusions:
- The combined array tomography and FIB-SEM tomography method overcomes previous limitations in analyzing deep biological structures.
- This technique enables detailed visualization of cellular ultrastructure, such as chondrocyte surface morphology.
- The method shows significant promise for mesoscopic architectural analysis, especially when combined with immunostaining.
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