data explosion in medical imaging
DESCRIPTION
A talk at The Fifth Elephant - a confrence on Big Data in Bangalore - July 2012TRANSCRIPT
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Data Explosion in Medical ImagingShourya SarcarSr. Engineering ManagerGE Healthcare
@shouryasarcar
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Rene Laennec , "immediate" auscultation with the unaided ear
1820Paris
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2010Handheld
digital ultrasound
stethoscope
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Imaging 101
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Digital X-Ray
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Computed Tomography
X-Ray technology, but in 3D !
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Magnetic Resonance Imaging
• Principal of magnetic spin• Great for soft tissue imaging
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Positron Emission Tomography
PET-CT
• Functional imaging• Radioactive bio-marker
binds to cancerous cell• Capture positron decay
with a scintillation detector
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Digital Acquisition System
Image Reconstruction
Add Patient Information
Basic Imaging Chain
The fancier the DAS, The larger the data
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How BIG is that Image Data ?
Pixel
Header
1024 x 102416 bits per pixel2 MB(tchah ! That’s not much)
Primarily “Text”Few KB
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They don’t come alone !
Images come in “Stacks”, a.k.aVolumesSeriesSlices
HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
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How BIG is that Image Data ?
Full body PET CT Cardiac fMRI
Images / set 600 3000 20000
Size of 1 set 1.2 GB 6 GB 40 GB
No. of sets (typical)
4 6 8
Exam Size 9 GB 36 GB 300 GBSizes are approximations
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How do we take that data home ?
…and who does it belong to ?
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To store and
share digital data,
we need a
format and a
protocol
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And there was none until 1993 !
“And the whole earth was of one language and of one speech” ~ Genesis 11
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DICOM: Digital Information and Communication in Medicine
1985 1988 1993
ACR-NEMA 1.0 ACR-NEMA 2.0 DICOM 3.0
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DiagnosticImaging
DICOM Scope
PatientBedside
Monitoring
Administrative HIS/RIS
. . .
Lab Data
. . .
Medical Informatics
Scope ofDICOM
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DICOM Standard
PS 3.1: Introduction and Overview
PS 3.2: Conformance
PS 3.3: Information Object Definitions
PS 3.4: Service Class Specifications
PS 3.5: Data Structure and Encoding
PS 3.6: Data Dictionary
PS 3.7: Message Exchange
PS 3.8: Network Communication Support for Message Exchange
PS 3.9: Point‑to‑Point Communication Support for Message Exchange (Retired)
PS 3.10: Media Storage and File Format for Data Interchange
PS 3.11: Media Storage Application Profiles
PS 3.12: Storage Functions and Media Formats for Data Interchange
PS 3.13: Print Management Point-to-Point Communication Support (Retired)
PS 3.14: Grayscale Standard Display Function
PS 3.15: Security Profiles
PS 3.16: Content Mapping Resource
PS 3.17: Explanatory Information
PS 3.18: Web Access to DICOM Persistent Objects
PS 3.19: Application Hosting
PS 3.20: Transformation of DICOM to and from HL7 standards
20parts
161 supplemen
ts
+
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DICOM Network:where is it in the network stack?
Medical Imaging Application
DICOM Application Entity
DICOMUpper Level
Protocolfor TCP/IP
TCP
IPStandard Network Physical Layer(i.e. Ethernet, FDDI, ISDN, etc.)
OSI Association ControlService Element (ACSE)
OSI Presentation Kernel
OSI Session Kernel
OSI Transport
OSI Network
LLC
OSIstack
TCP/IPstack
OSI upper layerService boundary
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The Stack has Evolved !
Once Upon a
Time
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How much disk space is needed for cardiac screening
of Bangalore ?
Back of the envelope calculations
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Population of Bangalore : 7,000,000
Cardiac Screening : 50%
HDD / CT Cardiac : 20 GB
I need some space : 70 PB
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0
100
200
300
400
500
600
700
800
900
20
220
312
468
850
Data Stores in Tera Bytes
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Christian Medical College Vellore
0.5 million exams / yr60 TB
Clalit Healthcare Services, 14-hospital network in Israel
4.5 million exams/yr
250 TB (annually)
Est. imaging data size in US – 2014
100 PB
Est. imaging data size globally – 2020
35 ZB
Some more size estimates
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Challenges of Large Imaging Data
Archival Search Transfer
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Lawmakers demand storage guarantee
Moms:“25 years after the birth of the last child”
Mentally disabled:“20 years after the last contact or 8 years after the patient's death”
Children: “Until the patient is 25”
Storage Commitment built into DICOM
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Huge Capacity requirements
Huge CapExUnpredictable TCOHardware technology obsoSpaceData-center grade infra
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Simple search is a soft problem
Index only the meta-data DICOM loves SQL
Finding the needle in the haystack
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HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
HeaderPixel
SQL Tables
Flat Files Power of SQL queries Insertion is fast, Read is
fast Replicate tables Memory-mapped IO Better disaster
recovery
Relevant header info
Complete File
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Why move the data ?
• Offline storage [Store/Fetch]• Reporting• Teleradiology / Remote
reporting
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Remote Radiologist
Onsite Radiologist
Outpatient Imaging Center
Inte
rnet
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Why move the data ?
• Offline storage [Store/Fetch]• Reporting• Teleradiology / Remote
reporting
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Challenges of DICOM
• DICOM is based on TCP/IP• Slow over large number of hops• FileCatalyst, CISCO WAAS
• DICOM compression is not adequate• Lossy, Loseless
• DICOM is not efficient on fault-tolerance• Dated retry mechanism, transmit
in sets/series, not files
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FOSS DICOM Tools and Images
ftp://medical.nema.org/medical/dicom/DataSets/
http://www.barre.nom.fr/medical/samples/
OsiriX for MacSantesoft for WinKradview for Linux
Language Toolkit
C/C++ GDCM, DCMTK
Java Pixel, dmc4che
Perl DICOM.pm
Ruby Ruby DICOM
Python pydicom
PHP Nanodicom
C# DICOM#
Viewers
Public Datasets
API
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