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“Live” Tomographic Reconstructions

Date post: 02-Jan-2016
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“Live” Tomographic Reconstructions. Alun Ashton Mark Basham. Incentive. Higher resolution cameras are forcing larger collection times. - PowerPoint PPT Presentation
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“Live” Tomographic Reconstructions Alun Ashton Mark Basham
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  • Live Tomographic ReconstructionsAlun AshtonMark Basham

  • OverviewIncentiveExperimental ChangesBeamline OverviewReconstruction HardwareConclusions

  • IncentiveHigher resolution cameras are forcing larger collection times.I12 at DLS will use a 4000x2500 pixel detector (PCO 4000) capable of approximately 2 frames per second (Technically 4-5 frames). Assuming the best case scenario this will require around 30-40 minutes to collect the data(~4000 images i.e. the width of the detector). Even with good cluster performance, it could still take around 30 minutes to make the 80GB reconstructed volume (4000x4000x2500)

    Having to wait an hour from start to finish before being able to see what has been imaged is frustrating, and could waste beam time due to misalignments etc.

  • Trying something differentRecent work has focused on fast and accurate reconstructions.Make good use of complete data sets to correct for various anomalies.This has to happen after the collection has been completed (on an 80Gb file)This work focuses on providing a reconstruction during the data collection.Less quality, and smaller reconstructions (e.g. 1000x600) to allow visualisation.Gives the user the ability to see the volume after only a few minutes.

  • Traditional TomographyIngoing PathOutgoing PathDirection of the beam

  • Traditional TomographyEach new acquisition collects the next segments data

  • Traditional Tomography

  • Traditional Tomography

  • Traditional Tomography

  • Traditional TomographyAll the data has been collected and the final full size and quality reconstruction can be produced

  • Experimental changesTo make the maximum use of this methodology there needs to be some experimental changes.The main change is in the way that the data is collectedThis requires certain hardware requirements mainly a sample stage capable of continuous rotationThe acquisition is then preformed as follows

  • Continuous rotationIngoing PathOutgoing Path

  • Continuous rotationEach new acquisition skips 4 segments and then collects the 5th

  • Continuous rotation

  • Continuous rotationInitial lowest quality reconstruction can now be calculated

  • Continuous rotationBecause its transmition you can flip the image and then its going the right way. So becomes red

  • Continuous rotation

  • Continuous rotation

  • Continuous rotationRefined reconstruction can now be calculated and replaces the previous one.

  • Continuous rotationThis is where skipping 4 becomes important.

  • Continuous rotation

  • Continuous rotationRefined reconstruction can now be calculated and replaces the previous one.

  • Continuous rotation

  • Continuous rotation

  • Continuous rotation

  • Continuous rotationRefined reconstruction can now be calculated and replaces the previous one.

  • Continuous rotation

  • Continuous rotation

  • Continuous rotationAll the data has been collected and the final full size and quality reconstruction can be produced

  • Progressive CollectionAdvantagesA full reconstruction can be preformed after only a fifth of the acquisition time, albeit at reduced resolution.As there is a gap between acquisitions, the full sector can be integrated, then the gap can be used for camera readout.DisadvantagesRequires custom software to reconstruct, or convert to classical data.If the gap is too large, acquisition time can be increased.

  • Integration TimeSector 1Sector 2S1S2TraditionalNewAcquisitionDetector tomemoryAcquisitionDetector tomemoryTime

  • ArchitectureBeamline Control PCCamera Control and Live Reconstruction PCCentral StorageCluster Computing ResourcesDigital camera

  • ArchitectureStart-up

  • ArchitectureStart-up

  • ArchitectureCollect Images

  • ArchitectureEnd of collection

  • ArchitectureProduce full reconstruction

  • Differences to normal setups

  • Computing Hardware for the live reconstructionStandard PC serverPasses the data on to the central storageScales and applies the flat field correction to the images as they come in.Runs the Host program for the TeslaTesla Graphics Processor UnitTakes the scaled and corrected imagesFilters the images.Provides the Back Projection.

  • Why the TESLATomography is inherently very parallelisableTesla requires around 100,000 concurrent threads to make it effectiveThis then allow for in general a single GPU to run 40 times faster on these problems than a single CPU or 10 times faster then a QuadCore.Space and power are saved in this case as a 1U Tesla Unit can effectively replace 20 dual processor quad core machines, for tomographic reconstruction.This also allows our beamline machine to pack the punch required to make the live reconstructions possible.

  • ConclusionsThis methodology for collecting tomographic data should give the users much more insight into there samples and more time to make decisions about collections.

    The Tesla GPU is a good way of increasing the speed of Tomographic reconstruction, and has been proven in various different labs around the world.

    We can modify the way in which the experiment is preformed to make the most use or influence the choice of hardware, such as the modifications made to allow for camera readout and continuous rotation stage.

  • AcknowledgementsManchester UniversityValeriy Titarenko, Albrecht Kyrieleis, Phil Withers, Mark Ibson.Diamond Light SourceMichael Drakopoulos, Thomas ConnolleyArchitecture Piercarlo Grandi, Nick Rees, Bill Pullford

    Mark Basham, [email protected]

    PCO = name of camera!Technically 4-5 frames a second 4000 images is the width of the detector.

    Full size reconstructions is an 80G file and that can take between 5 and 30 mins transferImportant bit is the continuous rotation sample stage. 5 means you collect all the data. Needs to be a prime? Skipping 4 collecting one means you collect all the data.No fancy artefact removal etc. only 1/5 of data.Within 7-8 mins you can see and check the collection.Because its transmition you can flip the image and then its going the right way. So red.


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