automatic volumetric breast density assessment in the extensible imaging platform rachel embree and...

Automatic Automatic Volumetric Breast Volumetric Breast

Density Density Assessment in the Assessment in the

eXtensible Imaging eXtensible Imaging PlatformPlatformRachel Embree and Christina Rachel Embree and Christina

SillerySilleryDavid Channin, MD, AdvisorDavid Channin, MD, Advisor

In Cooperation with Alex In Cooperation with Alex Shnayder, Pat Mongkolwat, Ray Shnayder, Pat Mongkolwat, Ray

WuWu

OverviewOverview

IntroductionIntroduction Material and MethodsMaterial and Methods ResultsResults DiscussionDiscussion ConclusionConclusion

IntroductionIntroduction

What is Breast Density?What is Breast Density? The breast is composed of fibroglandular tissue The breast is composed of fibroglandular tissue

embedded in a background of fatty tissue. The embedded in a background of fatty tissue. The amount of fibroglandular tissue and fat varies amount of fibroglandular tissue and fat varies among women.among women.

Breast cancer arises in this fibroglandular tissue.Breast cancer arises in this fibroglandular tissue. Mammography is projection radiography of the Mammography is projection radiography of the

breast.breast. In mammograms, dense fibroglandular tissue In mammograms, dense fibroglandular tissue

attenuates more radiation than does fat.attenuates more radiation than does fat. Breast density refers to the appearance of this Breast density refers to the appearance of this

fibroglandular tissue in a mammogram [5]fibroglandular tissue in a mammogram [5]

Breast DensityBreast Density

Positively correlated with breast Positively correlated with breast cancercancer FourFour to to sixsix times greater risk of breast times greater risk of breast

cancer for women with greater than cancer for women with greater than 60% dense tissue [1]60% dense tissue [1]

Breast density as a risk factor accounts Breast density as a risk factor accounts for as many as 30% of breast cancer for as many as 30% of breast cancer cases [1]cases [1]

Can be changed by hormonal, Can be changed by hormonal, dietary and other interventionsdietary and other interventions

Assessment of Breast Assessment of Breast Density in MammogramsDensity in Mammograms

Subjective Visual Assessment by Subjective Visual Assessment by Radiologists (Mandatory)Radiologists (Mandatory) Score the breast on a 4-point scale in Score the breast on a 4-point scale in

the Breast Imaging-Reporting and Data the Breast Imaging-Reporting and Data System (BIRADS), based on patterns System (BIRADS), based on patterns developed by Wolfe [5]developed by Wolfe [5]

Manual Image Processing Manual Image Processing Techniques (for research)Techniques (for research) PlanimetryPlanimetry Interactive ThresholdingInteractive Thresholding

Previous ApproachesPrevious Approaches Interactive ThresholdingInteractive Thresholding

GoalGoal

Create a breast density assessment Create a breast density assessment program that is…program that is… AutomatedAutomated VolumetricVolumetric AccurateAccurate In the eXtensible Imaging Platform In the eXtensible Imaging Platform

(XIP)(XIP)

Material and Material and MethodsMethods

What is XIP?What is XIP? eXtensible Imaging PlatformeXtensible Imaging Platform

Funded by NIH, NCI Cancer Bioinformatics Grid Funded by NIH, NCI Cancer Bioinformatics Grid (caBIG) Program(caBIG) Program

A program to share data, informatics tools, technologies A program to share data, informatics tools, technologies and infrastructure between the funded Comprehensive and infrastructure between the funded Comprehensive Cancer Centers across the nationCancer Centers across the nation

Open Source, Open Standards, Open Open Source, Open Standards, Open ArchitectureArchitecture

Platform for development of medical image Platform for development of medical image processing and analysis applications for processing and analysis applications for research and clinical purposes.research and clinical purposes.

Will support the DICOM Application Hosting Will support the DICOM Application Hosting standard to facilitate transportability of XIP standard to facilitate transportability of XIP applicationsapplications

XIPBuilderXIPBuilder

Visual Programming Environment for Visual Programming Environment for developing imaging applications; based on developing imaging applications; based on OpenInventor.OpenInventor.

Contains modules (lots!) that can be Contains modules (lots!) that can be assembled to perform sophisticated tasks. assembled to perform sophisticated tasks.

IncludesIncludes vTK – The Visualization Toolkit (NIH)vTK – The Visualization Toolkit (NIH) iTK – The Insight Toolkit for Registration and iTK – The Insight Toolkit for Registration and

Segmentation (NIH)Segmentation (NIH) Extensible by creating new plug-n-play Extensible by creating new plug-n-play

modulesmodules

MammographyMammography

Algorithmic FoundationsAlgorithmic Foundations

Highnam et al 1997Highnam et al 1997 Standard Mammogram Form (SMF)Standard Mammogram Form (SMF) Volumetric approachVolumetric approach Mammograms on X-ray filmMammograms on X-ray film

Van Engeland et al 2006Van Engeland et al 2006 Improved upon SMFImproved upon SMF Full Field Digital Mammography Full Field Digital Mammography

(FFDM)(FFDM) Utilized DICOM headersUtilized DICOM headers

The ModelThe Model

[2]

VolumetricVolumetric

Based on Van Engeland’s algorithm [4]Based on Van Engeland’s algorithm [4] Tissue composition is computed at each Tissue composition is computed at each

pixel and represents a rectangular pixel and represents a rectangular cylinder of tissuecylinder of tissue

Area of the pixel is computed from Area of the pixel is computed from detector characteristics and the geometry detector characteristics and the geometry of acquisition.of acquisition.

Height of the rectangular cylinder is Height of the rectangular cylinder is computed from the compression computed from the compression thickness.thickness.

RADBuilder ProcessRADBuilder Process

SoXIPLoadDICOM

SoItkBinaryThresholdImageFilter

SoXIPBreastTotalTissueVolume

Calculation

SoItkMultiplyImageFilter

SoXIPBreastDense

TissueVolumeCalculation

SoXIPLinearAttenuationCoefficients

Calculator Separator


SoXIPLoadDICOMSoXIPLoadDICOM Loads …Loads …

DICOM Image Pixel DataDICOM Image Pixel Data Necessary DICOM Header InformationNecessary DICOM Header Information


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





SoItkBinaryThresholdImagSoItkBinaryThresholdImageFiltereFilter

Each pixel compared to threshold Each pixel compared to threshold valuevalue

Output image of 0 and 1 valuesOutput image of 0 and 1 values

Input Output


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





SoItkMultiplyImageFilterSoItkMultiplyImageFilter

Pixel-wise multiplication of two Pixel-wise multiplication of two imagesimages

Lays background mask on top of Lays background mask on top of original imageoriginal image

Input 1 Input 2 Output


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





SoXIPLinearAttenuationCoeSoXIPLinearAttenuationCoefficientsfficients

Determines difference between Determines difference between effective attenuation of dense tissue effective attenuation of dense tissue and fatand fat

This Attenuation Difference This Attenuation Difference Coefficient is chosen from a table [4]Coefficient is chosen from a table [4] Based on DICOM header informationBased on DICOM header information

Anode target materialAnode target material Filter materialFilter material kVpkVp Breast ThicknessBreast Thickness


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





hhdd(r) : height of dense tissue at pixel (r) : height of dense tissue at pixel rr µµdd, eff, eff - - µµff, eff, eff : : Attenuation Difference CoefficientAttenuation Difference Coefficient

g(r) : current pixel valueg(r) : current pixel value ggff : fatty tissue reference value : fatty tissue reference value

SoXIPBreastDenseTissueSoXIPBreastDenseTissueVolumeCalculationVolumeCalculation

[4]

hhdd(r)(r) : height of dense tissue at pixel : height of dense tissue at pixel rr µµdd, eff, eff - - µµff, eff, eff : : Attenuation Difference CoefficientAttenuation Difference Coefficient



[4]




[4]


g(r)g(r) : current pixel value : current pixel value ggff : fatty tissue reference value : fatty tissue reference value


[4]




[4]

Where does fatty tissue Where does fatty tissue reference value, greference value, gf f , come , come

from?from? Maximum pixel value (minimum Maximum pixel value (minimum

attentuation) in the interior of the breast attentuation) in the interior of the breast (this should represent a pure fat pixel).(this should represent a pure fat pixel).

Calculate a histogram of the image.Calculate a histogram of the image. Select the pixel value at 80% (empirical Select the pixel value at 80% (empirical

determination) of the maximum pixel determination) of the maximum pixel values (avoids skin edges; low values (avoids skin edges; low attenuation due to incomplete attenuation due to incomplete thickness).thickness).


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





SoItkBinaryThresholdImagSoItkBinaryThresholdImageFiltereFilter

Adjust parameters to detect breast Adjust parameters to detect breast edge instead of entire regionedge instead of entire region

Input Output


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





SoXIPBreastTotalTissueSoXIPBreastTotalTissueVolumeCalculationVolumeCalculation

h(r) : total height of tissue at pixel h(r) : total height of tissue at pixel rr HH : compressed breast thickness : compressed breast thickness d(r) : Euclidean distance to the edge d(r) : Euclidean distance to the edge

between between breast tissue and breast tissue and backgroundbackground

[4]


h(r)h(r) : total height of tissue at pixel : total height of tissue at pixel rr HH : compressed breast thickness : compressed breast thickness d(r) : Euclidean distance to the edge d(r) : Euclidean distance to the edge


[4]


h(r) : total height of tissue at pixel h(r) : total height of tissue at pixel rr HH : compressed breast thickness : compressed breast thickness d(r) : Euclidean distance to the edge d(r) : Euclidean distance to the edge


[4]


h(r) : total height of tissue at pixel h(r) : total height of tissue at pixel rr HH : compressed breast thickness : compressed breast thickness d(r)d(r) : Euclidean distance to the edge : Euclidean distance to the edge


[4]


If Euclidean distance is less than If Euclidean distance is less than half of breast compression …half of breast compression … use first formula in calculation of total use first formula in calculation of total

tissue volumetissue volume

[4]


If Euclidean distance is greater than If Euclidean distance is greater than half of breast compression… half of breast compression… use breast compression in calculation of use breast compression in calculation of

total tissue volumetotal tissue volume

[4]


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





CalculatorCalculator

Module in XIPBuilderModule in XIPBuilder

Dense Tissue VolumeDense Tissue Volume

Total Tissue Volume Total Tissue Volume x 100 = Percent Density


SoXIPLoadDICOM



Calculation


SoXIPBreastDense





SeparatorSeparator

Module in RADBuilderModule in RADBuilder Displays outputDisplays output

In this case, textIn this case, text

Methods IIMethods II

20 CC full-field digital mammograms20 CC full-field digital mammograms Prior manual breast density assessment Prior manual breast density assessment

using ImageJusing ImageJ Determine breast density using Determine breast density using

Cumulus™, a popular interactive Cumulus™, a popular interactive thresholding programthresholding program

Determine breast density with the Determine breast density with the automated XIP solutionautomated XIP solution

Methods IIIMethods III

Compare the three measurements of Compare the three measurements of breast density to determine breast density to determine Kendall’s Coefficient of ConcordanceKendall’s Coefficient of Concordance

Use that coefficient to determine a Use that coefficient to determine a χχ2 2 that allows testing of the null that allows testing of the null hypothesis:hypothesis:

There is no agreement in the There is no agreement in the assessment of breast density by assessment of breast density by

the three methodsthe three methods

ResultsResults

The overall Kendall’s Coefficient The overall Kendall’s Coefficient comparing the three systems was comparing the three systems was 0.5020.502

For 20 cases and three systems, the For 20 cases and three systems, the χχ2 2 is 57.276 which allows the is 57.276 which allows the rejection of the null hypothesis (rejection of the null hypothesis (χχ2 2 of of 30.14, 19 degrees of freedom, 30.14, 19 degrees of freedom, αα =0.05).=0.05).

ConclusionConclusion

It was possible to develop, in XIP, an It was possible to develop, in XIP, an automatic software application to automatic software application to measure volumetric breast density in measure volumetric breast density in mammograms.mammograms.

The automatic measurement agreed The automatic measurement agreed well with two, independent, manual well with two, independent, manual thresholding based techniques in thresholding based techniques in common, current use.common, current use.

Future WorkFuture Work

MLO view capabilityMLO view capability Anisotropic FilterAnisotropic Filter Improve fatty reference value Improve fatty reference value

identificationidentification Validate this and other techniques Validate this and other techniques

against ground truth (MRI)against ground truth (MRI)

ReferencesReferences1.1. Boyd, N., Lockwood, G., Byng, J., Tritchler, D., Yaffe, M., Boyd, N., Lockwood, G., Byng, J., Tritchler, D., Yaffe, M.,

“Mammographic Densities and Breast Cancer Risk”. “Mammographic Densities and Breast Cancer Risk”. Cancer Epidemiology, Biomarkers & Prevention, 7, Cancer Epidemiology, Biomarkers & Prevention, 7, 1133-1133-1144.1144.

2.2. Marias K et al. “A Mammographic Image Analysis Method Marias K et al. “A Mammographic Image Analysis Method to Detect and Measure Changes in Breast Density”. to Detect and Measure Changes in Breast Density”. European Journal of RadiologyEuropean Journal of Radiology. 2004; 52:276-282.. 2004; 52:276-282.

3.3. Vacek, Pamela M., Geller, Berta M. (2004) A Prospective Vacek, Pamela M., Geller, Berta M. (2004) A Prospective Study of Breast Cancer Risk Using Routine Study of Breast Cancer Risk Using Routine Mammographic Breast Density. Mammographic Breast Density. Cancer Epidemiology, Cancer Epidemiology, Biomarkers & Prevention. 13(5). Biomarkers & Prevention. 13(5). 715-722.715-722.

4.4. Van Engeland, S., Snoeren, P.R., Huisman, H., Boetes, C., Van Engeland, S., Snoeren, P.R., Huisman, H., Boetes, C., Karssemeijer, N., (2004) A Prospective Study of Breast Karssemeijer, N., (2004) A Prospective Study of Breast Cancer Risk Using Routine Mammographic Breast Cancer Risk Using Routine Mammographic Breast Density. Density. Cancer Epidemiology, Biomarkers & Prevention. Cancer Epidemiology, Biomarkers & Prevention. 2006; 13(5):715-722.2006; 13(5):715-722.

5.5. Wolfe JN. “Risk for Breast Cancer Development Wolfe JN. “Risk for Breast Cancer Development Determined by Mammographic Parenchymal Pattern”. Determined by Mammographic Parenchymal Pattern”. Cancer.Cancer. 1976; 37:2486-92. 1976; 37:2486-92.

automatic volumetric breast density assessment in the extensible imaging platform rachel embree and...

Documents

assessment of breast

breast cancer cases

breast imagingreporting

dense fibroglandular

dense tissue

introduction slide

background of fatty

ray wu slide