Neuroblastoma Stroma Classification on theSony Playstation 3

Tim Hartley, Olcay Sertel, Mansoor Khan,

Umit Catalyurek, Joel Saltz, Metin Gurcan

Department of Biomedical Informatics

The Ohio State University

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The Cell BE processorDesigned at IBM in conjunction with Toshiba and Sony (processor for the PS3)The Cell is a 9 core chip with a shared L2 cacheOne PowerPC (PPE) coreEight Synergistic Processing Elements (SPE)High performance I/O to support data-intensive applications

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Cell BE parallelism

Levels of parallelismInstruction-level

parallelism via 128-bit vector operations

Thread-level parallelism via independent SPE processors

CPU-level parallelism for extreme-scale problems

Some image analysis algorithms are appropriate to be parallelized

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Image analysis on Cell Neuroblastoma Nerve cell cancer

predominantly affecting children

Microscope slides can be very large (> 40 GB)

One SPE equivalent to 2.13 GHz 64-bit Intel or AMD CPU for this application

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Details of Cell port for analysis

Image labelImage label

Input imageInput image

LA*B* conversionLA*B* conversion

LL

A*A*

B*B*

Statistical feature extractionStatistical feature extraction

LBP feature

LBP feature

Bhattacharyya distanceBhattacharyya distance

KNN classifierKNN classifier

Flowchart of stroma classification algorithm

Algorithm overview Image partitioned into tiles RGB to LAB transformation LBP feature calculation

Computationally expensive portions RGB to LAB transformation LBP feature calculation

Two stages to Cell analysis pipeline RGB->LAB and color-space statistics LBP feature calculation

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More details of Cell portInstruction-level parallelism

Vector operations in pipeline stagesThread-level parallelism

Multiple SPEs analyzing multiple tiles concurrentlyDynamic scheduling of operations on SPEs

CPU-level parallelismUse DataCutter to decouple tile I/O from analysisTiles are read from storage node(s) and pushed to PS3(s)

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Algorithm workflow

Disabled(yield) Reserved

Lab

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Demo

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Conclusion

Performance in analysis of Neuroblastoma slides Up to 6 times faster than regular CPU with PS3

Price/performance ratio is significantly better than regular CPU

Sony and IBM encourage Linux-based development with official Software Development Kits (SDK), Linux OS installation support

PlayStation is a registered trademark of Sony Computer Entertainment Inc.