Soybean developing floral complex imaged with the ZEISS Xradia Versa X-ray microscope showing the ovary with developing ovules surrounded by the anthers containing bright pollen grains.
X-Ray Imaging Applications for Life Sciences

Capture Internal Plant Structure without Sectioning

Cellular Level Insights with Full 3D Context

Understanding plant organ systems can provide insights into health parameters such as crop strength, longevity, cropping efficacy and size. Visualizing these components and how they develop, function and are influenced by external factors, helps to optimize plant health and yield. Non-destructive X-ray microscopy provides high resolution structural information from different plant components without needing to cut the specimens and remove the 3D context.1, 2

Image Courtesy of Dr. Keith Duncan, Donald Danforth Plant Science Center, USA

Exploring Seed Development

High resolution scan of a developing soybean seed imaged with the ZEISS Xradia Versa. The ovule is located in the ovary, which becomes the soybean pod as the seeds develop. Courtesy of K. Duncan, Donald Danforth Plant Science Center, USA.​

High Resolution Insights without Compromising the Seed​

The ZEISS Xradia range of X-ray instruments provides high contrast and resolution that enable the non-destructive capture of many different structures including roots, leaves, stems, inflorescence, and seeds. The two-stage magnification of ZEISS Xradia Versa X-ray microscope with multiple objective lenses provides cellular resolution in these plant specimens, whilst maintaining the full 3D context of that cellular detail.

Arabidopsis seed imaged using ZEISS Xradia Versa X-ray microscope and segmented in 3D using Dragonfly Pro.

Generate quantifiable data from 3D insights

Following high resolution acquisition, data can be segmented to enable quantification of the 3D data. Information such as number, size and distribution of starch granules can be performed from the high quality datasets using analysis packages such as Dragonfly Pro.

Investigating Inflorescence​

Developing floral structures of Arabidopsis at different length scales. The bright dots are pollen grains, and the ovary is the long, tall structure with numerous developing ovules (seeds) inside. Courtesy of K. Duncan, Donald Danforth Plant Science Center, USA.

Multiscale Imaging of Delicate and Complex Floral Structures​

Incredible insights into internal plant structures down to the cellular level can be generated with data collected with ZEISS Xradia Versa and processed with Dragonfly Pro image analysis software. This information is captured in the context of the whole plant as the specimen does not need to be cut down in size for image capture.

Imaging Roots

Root growing in soil. The entire 2 cm x 10 cm syringe barrel was imaged to identify regions of interest for subsequent higher resolution imaging. Courtesy of K. Duncan, Donald Danforth Plant Science Center, St Louis, USA.

Multiscale Imaging of Roots Growing in Soil

The development of root structures and their interaction with soil are key determinants of overall plant health and proliferation. However, the location of roots below the surface of the soil can make it difficult to capture the process of root development or see the roots in situ. The non-destructive nature of X-ray imaging makes it a wonderful technology for visualizing roots and root networks whilst growing in the soil. High-resolution X-ray microscopy using ZEISS Xradia Versa enables visualization of root structure down to the cellular level but within the context of the rest of the root.

Investigating Ways to Reduce Soil Erosion

Pennycress seed pod imaged with the ZEISS Xradia Versa, first with the 0.4x objective, and then the 4x objective. Courtesy of K. Duncan, Donald Danforth Plant Science Center, USA.​

Non-destructive Assessment of Pennycress​

Finding ways to reduce soil erosion and the run-off of fertilizer is important for maintaining soil quality and for optimizing crop yield at different locations. Pennycress is a species of plant that is being developed as a financially viable cover crop, planted between conventional commodity crops to reduce both erosion and fertilizer run-off, sequester carbon in the soil, and maintain favorable microbial populations in the soil. X-ray microscopy can be used to visualize the internal structures of pennycress without needing to physically section the plant.​

Exploring Soil Aggregates​

Soil aggregate inside a sample tube imaged undisturbed at multiple scales using ZEISS Xradia Versa. Courtesy of K. Duncan, Donald Danforth Plant Science Center, USA.

Capture the Structure of Soil Aggregates without Disturbance​

In addition to soil erosion, the impact of different land management practices on soil and soil aggregates is another important question. Non-destructive imaging using X-rays can be used to explore structures, interfaces and changes in 3D for a volume of soil. Exploring how land management practices impact the arrangement of soil and resulting plant health at multiple length scales provides interesting insights that cannot otherwise be achieved. Studies comparing soil from different land management practices such as No Till versus Conventional Till can be performed.

Improving Signal to Noise and Throughput of 3D Acquisitions​

Punch biopsy from a tobacco leaf. The 3001 2D projection dataset was reconstructed with traditional FDK (left)
Punch biopsy from a tobacco leaf. The 3001 2D projection dataset was reconstructed with DeepRecon (right)
Punch biopsy from a tobacco leaf. The 3001 2D projection dataset was reconstructed with traditional FDK (left) and DeepRecon (right). Courtesy of K. Duncan and K. Czymmek, Donald Danforth Research Center, USA.

Simultaneous Reduction of Noise and Acquisition Time with Deep Learning Reconstruction​

Deep Learning reconstruction increases both the signal to noise ratio of the reconstructed datasets and the overall throughput of the imaging approach. ZEISS DeepRecon requires far fewer 2D projection images for the final reconstruction, thereby reducing acquisition times and improving the µCT throughput by up to 10 times. ​

This significant performance improvement is possible without the need for any additional X-ray beam-line hardware. For plant science specimens, the increase in throughput is beneficial for every acquisition, and the increase in signal-to-noise ratio is particularly useful when the resolution is being pushed and structures of interest are otherwise shrouded by noise.

Imaging in Action

Donald Danforth Plant Science Center

  • Learn how the world’s largest independent non-profit plant research institute uses ZEISS Xradia Versa X-ray microscopes to explore inflorescence development, perform multiscale imaging of roots, and investigate ways to reduce soil erosion.


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