Integration of Software for 3D Tissue Reconstruction Based on Optical Probe Nanotomography Data

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Abstract

The task of three-dimensional (3D) reconstruction of tissues at the cellular and subcellular level is an integral part of modern biomedical research. Developing 3D reconstruction methods based on atomic force and optical microscopy images enables a more detailed understanding of the morphology and structure of biological specimens at the nanoscale. In the present study, we integrated dedicated software into the workflow of optically probed nanotomography (OPNT) to optimize and standardize the volumetric reconstruction process and demonstrated the capabilities of the enhanced method by reconstructing a fragment of an astrocyte in 3D. The incorporation of 3D Slicer into the OPNT protocol provides a reliable, high-precision platform for the three-dimensional reconstruction of complex biological structures. The proposed approach has practical utility for specialized tasks – such as evaluating the synaptic environment of individual neurons – as well as for a wide range of investigations in biomedical research and materials science.

About the authors

D. О Solovyevа

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry

Email: d.solovieva@mail.ru
Russia, Moscow

О. Y Popadinets

National Research Nuclear University MEPhI

Russia, Moscow

I. S Kolpashnikov

National Research Nuclear University MEPhI

Russia, Moscow

A. V Altunina

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry; Moscow Institute of Physics and Technology (National Research University)

Russia, Moscow; Russia, Dolgoprudny

V. A Oleinikov

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry; National Research Nuclear University MEPhI

Russia, Moscow

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