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Resources / Publication Spotlight / X-Ray Microscopy for Plants Across Multiple Resolution Scales

X-ray microscopy for plants across multiple resolution scales

Researchers from the Donald Danforth Plant Science Center in St Louis, Missouri in the USA recently published a comprehensive study entitled “X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs” in the journal Plant Physiology. This work demonstrates the use of X-ray microscopy to image plant samples across multiple resolution scales in three dimensions, including demonstrating multimodal correlative imaging workflows combining serial block face SEM and XRM, as well as advanced segmentation approaches. Dragonfly was used for registration of multiscale and multimodal imaging datasets, for 3D segmentation, visualization and advanced measurements. Overall the results demonstrate the huge potential for X-ray microscopy in plant sciences.

According to lead author Dr Keith Duncan, “Dragonfly is our first choice for 3D and multimodal image analysis. Dragonfly’s user interface is easy to manage and I was able to generate high quality images and animations in my first session with the software. We’re also using the Dragonfly Deep Learning functionality for many of our image analysis and segmentation projects. Dragonfly is a powerful tool that we have installed on all our imaging workstations, which is free for non-commercial users like us.”

Video Presentations


Keith E. Duncan, Kirk J. Czymmek, Ni Jiang, August C. Thies, Christopher N. Topp, X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs. Plant Physiology: Volume 188, Issue 2, February 2022, Pages 831–845 (

Associated Research Center

Donald Danforth Plant Science Center


The XRM is a powerful tool for imaging delicate and complicated structures like these developing Arabidopsis flowers. XRM allows visualization of pollen grains in anthers and elongated seed-bearing ovules, and how these structures are situated relative to each other in 3D space within the floral complex.


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