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2023 EMSL User Meeting
October 3 - 5, 2023

EMSL User Meeting: Visualizing Chemical Processes Across the Environment

October 3–5, 2023 | Pacific Northwest National Laboratory

Sessions also available online.

This engaging, three-day meeting (previously known as EMSL Integration) includes keynote speakers, contributor talks, flash talks, tutorials, and poster sessions encompassing the following topics: 

  • Biological Cartography: Building methods to map cellular and molecular processes across scales from microbes to the rhizosphere.

  • Spatially Resolved Integrative Omics: Revealing fundamental biological processes within cells and tissue functional units.

  • Multimodal Imaging: Refining and advancing the use of in situ tools in a synergetic fashion to address key environmental processes.

Presentation recordings are now available.

Abstract submissions 

Interested in sharing your research at the 2023 EMSL User Meeting? 

The Planning Committee is accepting abstracts for posters and contributed talks that generally focus on the following topics: 

  • Biological Cartography: Building methods to map cellular and molecular processes across scales from microbes to the rhizosphere.

  • Spatially Resolved Integrative Omics: Revealing fundamental biological processes within cells and tissue functional units.

  • Multimodal Imaging: Refining and advancing the use of in situ tools in a synergetic fashion to address key environmental processes.

Abstracts that don't neatly align with these research topics will also be considered. 

* Note that submitting an abstract does not register you for the meeting. You must also complete the registration form. 


11:59 p.m. Pacific daylight time on Friday, August 18, 2023 

Submit an abstract

Who should attend 

Researchers around the world from academia, industry, and government research laboratories are invited to attend. 

This meeting is open to EMSL users and non-users alike (you do not have to be a current EMSL user to attend). 

Registration rates

In-person     Virtual
General registration in-person: $300      General virtual registration: $200 
Student registration in-person: $150      Student virtual registration: $50 

Registration deadlines

  • Non-U.S. citizen: August 1 (Tuesday) 

Participants must be over the age of 18. 

Virtual participation 
Virtual meeting information will be provided to registered virtual attendees before the meeting. 


2023 EMSL User Meeting | Agenda

Tuesday, Oct. 3 | Day 1


7:30 a.m. – Registration and badging

8:30 a.m. – Opening remarks

8:45 a.m. – Overview of EMSL, capabilities, and user program

SESSION 1 | Mapping metabolic processes of environmental systems with spatially resolved mass spectrometry and mass spectrometry imaging

Session co-chairs: Dusan Velickovic and Robert Stanley

9:15 a.m. – Session 1 – Keynote #1

  • “Revealing the Intricacies of Organism-Environment Interactions using Spatial Metabolomics: A Path towards Understanding Adaptation and Acclimation”
    Malak Tfaily | Associate Professor | University of Arizona and EMSL

9:55 a.m. – Session 1 – Contributing talk #1

  • "A systems biology approach to reveal cell-type specific molecular responses to combined abiotic stresses in poplar"
    Vimal Kumar Balasubramanian | Biologist | EMSL

10:15 – Networking coffee break

10:30 a.m. – Session 1 – Contributing talk #2

  • "Integrating multi-omic and isotopic tools to map nitrogen metabolism in the sorghum rhizosphere"
    Holly Andrews | Postdoctoral Research Associate | University of Arizona

10:50 a.m. – Session 1 – Contributing talk #3

  • "A new in situ derivatization workflow for imaging carbonyls, phytohormones, and other hard to detect metabolites in environmental samples"
    Dusan Velickovic | Chemist | EMSL

11:10 a.m. – Session 1 – Keynote #2

  • "In vivo isotope labeling of plant metabolites for mass spectrometry imaging"
    Young-Jin Lee | Professor of Chemistry | Iowa State University

11:50 a.m. – Lunch and flash talks

  • Flash talks
    • "Developing and validating SPE-ICP-MS method for arsenic speciation analysis in groundwater" 
      Andrew Oroke | PhD Student Researcher | Newcastle University 

    • "Solution NMR spectroscopy identifies unique backbone dynamics in the Xanthamonas sacchari bacterial expansin EXLX1"
      Garry Buchko | Chemist | Pacific Northwest National Laboratory 

12:50 p.m. - User Executive Committee session

SESSION 2 | Spatial and multimodal omics analysis of plant systems

Session co-chairs: Vimal Kumar Balasubramanian and Amir Ahkami

1:50 p.m. – Session 2 – Keynote #1

  • “Enabling the Next Agricultural Revolution; Use of Single Cell Biology to Engineer Stronger, Healthier, and Better Crops”
    Marc Libault | Associate Professor | University of Nebraska-Lincoln

2:30 p.m. – Session 2 – Contributing talk #1

  • "Using small multiples to visualize and interact with leafcutter ant fungal garden multi-omics data"
    Lisa Bramer | Data Scientist | Pacific Northwest National Laboratory

2:50 p.m. – Group photo

3:05 p.m. – Networking coffee break

3:20 p.m. – Session 2 – Contributing talk #2

3:40 p.m. – Session 2 – Contributing talk #3

  • "Elucidating the molecular mechanisms of N-fixation by Populus Endophyte, Burkholderia vietnamiensis WPB"
    Jayde Aufrecht | Biologist | EMSL

4 p.m. – Session 2 – Keynote #2

  • “Single-cell and spatial dissection of plant-microbe interactions”
    Tatsuya Nobori | Human Frontier Science Program Postdoctoral Fellow | Salk Institute

4:40 p.m. – Poster session and evening networking reception | Sponsored by Thermo Fisher Scientific

  • Wine and light snacks served

Wednesday, Oct. 4 | Day 2


7:30 a.m. – Registration

SESSION 3 | Illuminating environmental processes using fluorescence microscopy tools

Session co-chairs: Dehong Hu and Lye Meng Markillie

8:30 a.m. – Session 3 – Keynote #1

  • "EMSL enabled studies of plant receptor function"
    Gary Stacey | Curators Distinguished Professor of Plant Science & Technology | University of Missouri

9:10 a.m. – Session 3 – Contributing talk #1

  • "Mapping microbial biogenic gas activity in peat soils at multiple scales of measurement using minimally invasive hydrogeophysical methods"
    Xavier Comas | Professor | Florida Atlantic University

9:30 a.m. – Session 3 – Keynote #2

  • “Spatial Metallomics and Metabolomics to Understand Metabolic Pathways of Plants and Cells involved in Bioenergy Processes”
    Yi Lu | Robert J.V. Johnson-Welch Regents Chair in Chemistry | University of Texas at Austin

10:10 a.m. – Networking coffee break

10:25 p.m. – Session 3 – Contributing talk #2

  • "Cellulose hydrolysis studied by infrared nanospectroscopy"
    Brian O’Callahan | Chemist | EMSL

10:45 a.m. – Session 3 – Contributing talk #3

  • "Fine root chemical plasticity in response to nutrient heterogeneity impacts root decomposition"
    Vidya Suseela | Associate Professor | Clemson University

SESSION 4 | Imaging environmental processes using advanced light sources

Session co-chairs: Arunima Bhattacharjee and Tamas Varga

11:05 a.m. – Session 4 – Keynote #1

  • "Deeper insights into calcium and potassium biogeochemical cycles from theory backed X-ray spectroscopy: An SSRL-EMSL collaboration"
    Ritimukta Sarangi | Senior scientist | SLAC National Accelerator Laboratory

11:45 a.m. – Session 4 – Contributing talk #1

  • "RhizoGrid root cartography spatially maps plant metabolite-microbe interactions in the Sorghum rhizosphere"
    Pubudu Handakumbura | Biologist | EMSL

12:05 p.m. – Lunch, flash talks, and posters

  • Flash talks: 
    • “Exploring the complexity of biological weathering with EMSL-based biogeochemical and mineralogical capabilities”
      Dragos Zaharescu | Assistant Project Scientist | University of California, Davis 

1:20 p.m. – Session 4 – Contributing talk #2

  • "Investigating the molecular processes controlling potassium translocation by fungi using synthetic soil habitats and synchrotron µ-XRF imaging"
    Jocelyn Richardson | Associate Scientist | SLAC National Accelerator Laboratory

1:40 p.m. – Session 4 – Keynote #2

  • "High-resolution X-ray microscopy techniques for environmental studies and microbiology at the Advanced Photon Source"
    Si Chen | Physicist | Argonne National Laboratory

2:20 p.m. – Session 4 – Contributing talk #3

  • "The use of multi-modal imaging for understanding plant-microbe interactions"
    Gyorgy Babnigg | Bioinformatician/Molecular Biologist | Argonne National Laboratory

2:40 p.m. – Networking coffee break

SESSION 5 | Revealing microscale and nanoscale environmental processes and interactions using electron microscopy

Session co-chairs: Jeremy Bougoure and Odeta Qafoku

2:55 p.m. – Session 5 – Keynote #1

  • "Molecular to micron scale investigations of colloids to understand field scale elemental transport"
    Ken Kemner | Senior Physicist | Argonne National Laboratory

3:35 p.m. – Session 5 – Contributing talk #1

  • "EMSL 1000 Fungal Proteins"
    James Evans | Chemist | EMSL

3:55 p.m. – Session 5 – Contributing talk #2

  • "Nanoscale defects and melting behaviors of ice revealed at atomic resolution"
    Jingshan Du | Washington Research Foundation Postdoctoral Fellow | Pacific Northwest National Laboratory

4:15 p.m. – Session 5 – Contributing talk #3

  • "Demystifying the molecular mechanisms of glycoside hydrolases by glycoproteomics"
    Stephanie Thibert | Postdoctoral Researcher | Pacific Northwest National Laboratory

4:35 p.m. – Session 5 – Keynote #2

  • "Cross-scale analyses of soil, fungi, and carbon delivered by advanced analytical capabilities"
    Rebecca Lybrand | Associate Professor | University of California, Davis

5:05 p.m. – Closing remarks

Thursday, Oct. 5 | Day 3

Workshops | Part 1 (hosted in EMSL)

8 a.m. – Synthetic soil habitats/TerraForms (30 people max)
EMSL 1075

  • Format: Presentation followed by in-lab activities.
  • Required attire: Long pants, at least half sleeves, and close-toed shoes. Safety glasses will be provided as needed.
  • Jayde Aufrecht | Biologist | EMSL
  • Arunima Bhattacharjee | Chemist | EMSL
  • Daisy Herrera | Postdoctoral Researcher | EMSL

8 a.m. – The potential of mass spectrometry imaging (40 people max)
EMSL Auditorium

  • Format: Presentation, interactive discussion, and panel discussion.
  • David Degnan | Data Scientist | PNNL
  • Kevin Zemaitis | Postdoctoral Researcher | EMSL

10 a.m. – Networking coffee break
Hosted in EMSL

Workshops | Part 2 (hosted in EMSL)

10:15 a.m. – Lifecycle of an EMSL user proposal: How to hatch your next big idea (30 people max)
EMSL Auditorium

  • Format: Presentation with audience engagement followed by two panels.
  • Rick Washburn | Project Manager | EMSL
  • Samantha Miller | Project Manager | EMSL

10:15 a.m. – Sample prep for imaging (24 people max)
EMSL 1075

12:15 p.m. – Working lunch – roundtable discussion
Discovery Hall

2 p.m. – EMSL tour
Begins in Discovery Hall

3:30 p.m. – End of meeting

Poster presenters

Poster sessions take place at 4:40 p.m. on Oct. 3 and 12:05 p.m. on Oct. 4 in Discovery Hall

  • Arctic climate change feedbacks: Analyzing the impact of increasing temperatures on microbial community assembly in the Arctic Permafrost Peatlands 
    Adeena Ahsan | Graduate Student | University of New Hampshire

  • Orthogonal mass spectrometry imaging techniques for more confident spatial identifications of small molecules 
    Rosalie Chu | Chemist | EMSL 

  • Applying high-resolution microscopy to explore fungal-grain interactions and distribution across contrasting mineral types 
    Cassandra Collins | University of California, Davis | Graduate student  

  • Evaluating post-fire changes in soil microbial communities involved in nitrogen cycling in the Arctic Tundra 
    Alma Hernandez | Graduate Student | University of New Hampshire 

  • Root volatile organic compound signatures in a semiarid sorghum agroecosystem 
    Linnea Honeker | Postdoctoral Research Associate | University of Arizona  

  • Metabolic pathway mapping and molecular phenotyping of biological and environmental systems through EMSL SIP-NMR and SIP-MS metabolomic capabilities 
    David Hoyt | Senior Research Scientist | EMSL 

  • Using X-ray computed tomography and chemical extractions to examine mineral weathering in rock substrates deployed along a bioclimate gradient 
    Madison Morris | Graduate Student | University of California, Davis 

  • Towards a general model for identifying particulate organic matter in X-ray microcomputed images of soil aggregates 
    Devin Rippner | Research Soil Scientist | U.S. Department of Agriculture 

  • Investigating the rate of horizontal gene transfer in the rhizosphere and environmental factors impacting it using fabricated ecosystems 
    Priya Shweta | Postdoctoral Biologist | Lawrence Berkeley National Laboratory 

  • Soil porous microstructure control over soil organic matter mobility: the case of two arid soils 
    Tamas Varga | Materials Scientist | EMSL 

  • Deep spatial metabolomics for confidential molecular identification in environmental samples 
    Marija Velickovic | Chemist | EMSL 

  • Electrochemically active biofilm in soil systems 
    Christina Webster | Graduate Student | Washington State University 

  • Elucidating the reaction pathways of veratrylglycero-β-guaiacyl ether degradation over metal-free solid acid catalyst with hydrogen 
    Bin Yang | Professor | Washington State University 

  • Emerging technologies: discovery proteomics by intact proteoform mass spectrometry imaging 
    Kevin Zemaitis | Postdoctoral Researcher | EMSL 

  • Chemical composition, coordination, and stability of Ca (bicarbonate) organic associations in the presence of dissolving calcite 
    Qian Zhao | Earth Scientist | EMSL 

  • Structural biology of plant cell wall biosynthetic enzymes 
    Samantha Ziegler | Research Scientist | National Renewable Energy Laboratory 


EMSL User Meeting Workshops

Thursday, Oct. 5

Workshop sign-ups are first-come, first-served.

Were you not asked for your workshop preference while completing your registration form (did you register prior to Aug. 8)?
Follow the instructions below to sign up for workshops of your choice.

Workshops Part 1

8 a.m. - Synthetic Soil Habitats / TerraForms Workshop - EMSL 1075

(30 people max)  

Organizers: Jayde Aufrecht, Arunima Bhattacharjee, and Daisy Herrera  

Format: Presentation followed by in-lab activities   

Required attire: Long pants, at least half sleeves, and close-toed shoes. Safety glasses will be provided as needed.


  • What are synthetic soil habitats / TerraForms (presentation)  

  • Designing a habitat   

  • Soft-lithography customization    

  • Prepping microhabitats   

  • Biological applications  

  • Downstream analyses   

8 a.m. - The Potential of Mass Spectrometry Imaging - EMSL Auditorium

(40 people max)  

Organizers: David Degan and Kevin Zemaitis  

Format: Presentation, interactive discussion, and panel discussion  


  • Introduction presentation 

    • Method overview, pipeline, and state of the field   

    • Instrument & computational aspects of:

      • How mass spectrometry imaging is different from other types of imaging

      • How mass spectrometry imaging is similar to other types of imaging  

    • Combining different kinds of imaging data  

  • Survey and survey-lead panel discussion   

Workshops Part 2

10:15 a.m. - Lifecycle of an EMSL User Proposal: How to Hatch Your Next Big Idea - EMSL Auditorium

(30 people max)  

Organizers: Rick Washburn, Samantha Miller, and Sarah Leichty  

Format: Presentation with audience engagement followed by two panels  


  • Presentation   

  • Lifecycle from letter of intent to full proposal approval   

  • Discuss changes to the proposal process including dual anonymous peer review and new submission templates  

  • Panel 1: Getting a handle on scope  

  • Ask integrated research platform leaders your questions about appropriate scope for EMSL user projects   

  • Panel 2: Crafting compelling proposals with the people who review them  

  • Previous user proposal reviewers and Science Area Leads discuss proposal dos and don'ts   

10:15 a.m. - Sample preparation for imaging - EMSL 1075

(24 people max)  

Organizers: Vimal Balasubramanian, Dusan Velickovic, Robert Stanley, Dehong Hu, Will Chrisler, Meng Markillie, and Odeta Qafoku  

Format: Presentation followed by in-lab activities   

Required attire: Long pants, at least half sleeves, and close-toed shoes.


  • Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)  

  • Fluorescence microscopy and laser capture microdissection (LCM)  

  • Electron microscopy and high-lateral resolution secondary ion mass spectrometry (NanoSIMS)   

Did you register and were not asked for your workshop choice?

If you have not already registered for the user meeting, you can select your in-person workshop of choice during registration. 

If you have already registered (and were not asked to sign up for an in-person workshop), visit the website and sign in.
To do so, please complete the following steps: 

  1. Click on the “Already registered?” link on the top right of the screen. You will then be prompted to enter your email address (be sure it’s the same email you registered with) and your confirmation number. Click Log In. 

  1. Scroll down and click the "Modify Registration" button 

  1. Click "Next" until you see the “Workshop registration” screen. 

  1. Select the workshops you’d like to register for and follow the prompts. 



A block of rooms has been arranged at the following hotel at the government per diem rate. The meeting registration fee does not include lodging. Hotel reservations should be made using the following information: 

TownePlace Suites by Marriott Richland Columbia Point 
591 Columbia Point Drive, Richland, WA 99352 
Distance to PNNL: 7.1 miles 
* Make your reservation in the group block by September 13, 2023 (Friday) 
Make an online reservation

Additional lodging options 

Holiday Inn Richland on the River 
802 George Washington Way, Richland, WA 99352 
Distance to PNNL: 5.3 miles 

Hampton Inn Richland/Tri-Cities 
486 Bradley Boulevard, Richland, WA 99352 
Distance to PNNL: 5.9 miles 

Travel information 

Tri-Cities Airport | Located in Pasco, WA (15.2 miles from PNNL) 

  • Rental Cars available 

  • Taxi Services 

  • On Time Taxi (509) 460-6850 

  • Rad Cab (509) 585-2944 

  • Tri-City Cab (509) 222-9208 

  • Uber and Lyft 

Local attractions 

Located in the heart of Washington wine country and on the convergence of three rivers, the Tri-Cities is home to a variety of activities and attractions. 

Check out the local attractions in the Tri-Cities!