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Building the Connectome – Guest Keynote, Part 2: "Brains and Globus"

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This presentation was given as part of a keynote address at the 2019 GlobusWorld Conference in Chicago, IL by Rafael Vescovi, Postdoctoral Scholar at Argonne National Laboratory and Bobby Kasthuri, Neuroscience Researcher, Argonne National Laboratory, Assistant Professor in Neurobiology, University of Chicago.

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Building the Connectome – Guest Keynote, Part 2: "Brains and Globus"

  1. 1. May 1st, 2019 GlobusWorld RAFAEL VESCOVI, PHD BRAINS AND GLOBUS Past, Present and Future..
  2. 2. 3 YEARS AGO A student came from Brazil to do tomography… • 1-5 minutes acquisition • 10-20 minutes of computation • 10 minutes for analysis • 10gb of raw+final data
  3. 3. XRAY RECONSTRUCTION OF THALAMO- CORTICAL SAMPLE 3
  4. 4. XRAY RECONSTRUCTION OF CORTEX SAMPLE
  5. 5. SEGMENTATION OF CORTEX SAMPLE
  6. 6. THE NECESSITY ▪Multiple samples ▪Multiple users ▪Multiple experiments – X-ray Tomography – Electron Microscopy – MRI ▪Different User levels – Beamline physicists – Biologists – HPC power users ▪Distribution of large amounts of data ▪Managing all of the above
  7. 7. THE SOLUTION • Each user/group has its own folder and group. • Permissions are given by the user itself • No need for power users
  8. 8. Storage Visualizing!! THE BASIC PIPELINE Camera PC1 PC2 Processing!! Decision The average time per sample was around 1 hour.
  9. 9. GLOBUS AUTOMATE
  10. 10. THE BASIC PIPELINE Camera PC1 PC2 Storage HPC Visualization Decision Without having to transfer, process and decide. The time per sample is only limited by the time it takes to acquire the data!!
  11. 11. GLOBUS DATA PORTAL
  12. 12. FUTURE IMPLEMENTATIONS ▪Real time data processing –1Pb/month –Minimal user interaction –Integration of web apps for visualization and tracing ▪Portal for different types of data –With trigger capabilities
  13. 13. FUTURE EM PIPELINE 13
  14. 14. AUTOMATIC VESSEL SEGMENTATION Demovessels.kasthurilab.com
  15. 15. AUTOMATIC CELL SEGMENTATION Democells.kasthurilab.com
  16. 16. ELECTRON MICROSCOPE SEGMENTATION 16
  17. 17. WHOLE MOUSE BRAIN X-RAY Wholebrain.kasthurilab.com 17
  18. 18. WHOLE MOUSE BRAIN X-RAY Cells and dentrites 18
  19. 19. www.anl.gov THANK YOU ALL!

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