Building the Connectome – Guest Keynote, Part 2: "Brains and Globus"
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May. 15, 2019•0 likes•374 views
Building the Connectome – Guest Keynote, Part 2: "Brains and Globus"
May. 15, 2019•0 likes•374 views
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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. May 1st, 2019 GlobusWorld RAFAEL VESCOVI, PHD BRAINS AND GLOBUS Past, Present and Future..
- 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. XRAY RECONSTRUCTION OF THALAMO- CORTICAL SAMPLE 3
- 4. XRAY RECONSTRUCTION OF CORTEX SAMPLE
- 5. SEGMENTATION OF CORTEX SAMPLE
- 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. THE SOLUTION • Each user/group has its own folder and group. • Permissions are given by the user itself • No need for power users
- 8. Storage Visualizing!! THE BASIC PIPELINE Camera PC1 PC2 Processing!! Decision The average time per sample was around 1 hour.
- 9. GLOBUS AUTOMATE
- 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. GLOBUS DATA PORTAL
- 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. FUTURE EM PIPELINE 13
- 14. AUTOMATIC VESSEL SEGMENTATION Demovessels.kasthurilab.com
- 15. AUTOMATIC CELL SEGMENTATION Democells.kasthurilab.com
- 16. ELECTRON MICROSCOPE SEGMENTATION 16
- 17. WHOLE MOUSE BRAIN X-RAY Wholebrain.kasthurilab.com 17
- 18. WHOLE MOUSE BRAIN X-RAY Cells and dentrites 18
- 19. www.anl.gov THANK YOU ALL!