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ARS Home » Southeast Area » Raleigh, North Carolina » Plant Science Research » Research » Publications at this Location » Publication #365893

Research Project: Genetic Improvement of Small Grains and Characterization of Pathogen Populations

Location: Plant Science Research

Title: Using pixel-based microscope images to generate 3-D reconstructions of frozen and thawed plant tissue

item Livingston, David
item Tuong, Tan

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 9/15/2019
Publication Date: 3/3/2020
Citation: Livingston, D.P., Tuong, T.D. 2020. Using pixel-based microscope images to generate 3-D reconstructions of frozen and thawed plant tissue. Plant Cold Acclimation: Methods and Protocols. Springer Protocols, Second Edition. Book Chapter. pgs. 119-139.

Interpretive Summary: 3D reconstruction of plant tissues using medical imaging techniques has been impossible due to the need for higher resolution to see internal structures of plants. In this book of Methods used in Cold Acclimation we present a technique we developed to generate 3D images of plants from conventional histological sections that have been stained to reveal internal structures. A complete and detailed tutorial is presented using the commercially available software Adobe After Effects. The technique is also suited for medical histological samples that may be too small for MRI or CT but too big for Confocal Microscopy.

Technical Abstract: Histological analysis of frozen and thawed plants has been conducted for many years but the observation of individual sections only provides a 2-dimensional representation of a 3-dimensional phenomenon. Currently available optical sectioning techniques for viewing internal structures in three dimensions are either low in resolution or the instrument cannot penetrate deep enough into the tissue to visualize the whole plant. Methods using higher resolution equipment are expensive and often require time-consuming training. In addition, conventional stains cannot be used for optical sectioning techniques. We present a relatively simple and less expensive technique using pixel-based (JPEG) images of conventionally stained histological sections of an Arabidopsis thaliana plant. The technique uses commercially available software to generate a 3D representation of internal structures.