Using Synchrotron Light to Probe Plant, Soil, and Geologic Systems.

x-ray ct of leaf tissues segmented by machine learning

Using Synchrotron Light to Probe Plant, Soil, and Geologic Systems. 

Workshop/Tutorial at the ALS User Meeting 2020, August 28, 2020

Organizers: Dr. Devin Rippner (USDA) (,, Dr. Tamas Varga, (EMSL, PNNL) (, Dr. Mengqiang Zhu (UWyo) (


Synchrotron light is used to probe chemical heterogeneity of geologic materials at the nanometer scale, investigate and resolve elemental composition and speciation in soils and plants, and study soil aggregate structure and plant hydraulics. This workshop aims to highlight some of the diverse uses of synchrotron light for investigating environmental systems with the goal of cross beamline collaboration for a more holistic understanding of environmental processes. As part of this workshop, presentations from Dr. Hans Bechtel and users of beamlines 1.4/2.4 will discuss applying micro and nano-fourier transform infrared spectroscopy (µ/nFTIR) to study mineral-organic matter associations at the nm to µm scale. Presentations from Dr. Sirine Fakra and users of beamline 10.3.2 will focus on using micro-focused X-ray absorption spectroscopy (µXAS) , X-ray fluorescence spectroscopy (µXFS) and microscopy techniques to study metal (Fe, Cu) and metal(loid) (P, As, Se, Cr) distribution and speciation in a variety of environmental systems. Presentations from Dr. Dula Parkinson and users of beamline 8.3.2 will discuss applying micro-x-ray computed tomography (µXCT) to porous media and plant systems. At the end of the day, a panel of beamline scientists and users from a variety of beamlines will discuss how to enable data collection on multiple beamlines to better improve our understanding of complex environmental processes.

Register Here!


micro-x-ray ct of soil aggregate with organic matter penetrating the aggregate.x-ray fluorescence microscopy image of copper oxide particle distribution in soils

Workshop Agenda:

Zoom Link!

8:00 Welcome, opening remarks (Devin/Tamas/ Mengqiang)

8:20 "Recent work at beamline 8.3.2"

Dr. Dula Parkinson (LBNL) (confirmed)

8:55: "How in situ synchrotron X-ray microtomography can help in improving the recovery of oil and gas in shale reservoirs"

Dr. Marco Voltolini (LBNL) (Confirmed)

9:30: “Photosynthesis to Starch Storage: New Techniques in Plant Physiology using X-ray MicroCT”

 Dr. Mason Earles (UCD) (Confirmed)

9:50 Break (10 min)

10:00: "Recent environmental research at the ALS 10.3.2 X-ray fluorescence microprobe"

Dr. Sirine Fakra (LBNL) (Confirmed)

10:35: "Using XAS and complementary methods to probe the speciation of phosphorus and iron in environmental samples"

Morgan Barnes (UCM) and  Dr. Peggy O’Day (UCM) (Confirmed)

11:10:  "Understanding the evolution of biogeochemical cycles across time and space using µ-XRF imaging"

Dr. Jocelyn Richardson ( SLAC) (Confirmed)

11:30: "Quantification of free- and metal bound-soil organic phosphorus during the ecosystem development"

Than Dam (UWyo) (Confirmed)

11:50: Lunch

12:50 "Synchrotron Infrared Micro- and Nano- spectroscopy at the ALS"

Dr. Hans Bechtel (LBNL) (Confirmed)

1:25: "SR-FTIR studies of bio-mineral microenvironments"

Dr. Patricia Valdespino-Castillo  (LBNL) (Confirmed)

2:00 "Deep look into deep permafrost:  SR-FTIR Spectromicroscopy characterization of microbial organic matter degradation"

Dr. Neslihan Taş (LBNL) (Confirmed)

2:20 Break (10 min break)

2:30 Panel Discussion to talk about potential for cross beamline collaboration (Can we invite more people to be on the panel?)

4:00 wrap up.

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