small intestine villi cell counting meghan olson & jittapat bunnag
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Small Intestine Villi Cell Small Intestine Villi Cell Counting Counting
Meghan OlsonMeghan Olson
& &
Jittapat BunnagJittapat Bunnag
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Background/MotivationBackground/Motivation
Research on Anemia (body can’t Research on Anemia (body can’t sufficiently distribute oxygen=> lack of sufficiently distribute oxygen=> lack of iron)iron)
Count cells that absorb iron (blue)Count cells that absorb iron (blue)• Currently counted manuallyCurrently counted manually
Time consumingTime consuming Inaccurate (different people count differently)Inaccurate (different people count differently)
Automated program would be idealAutomated program would be ideal• Standardized counting procedureStandardized counting procedure• Less time consuming to researcherLess time consuming to researcher
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GoalGoal
Count number of Count number of iron-absorbed iron-absorbed (blue) cells(blue) cells
Measure blue and Measure blue and red area, and red area, and calculate calculate percentagepercentage
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ComplexityComplexity Cell size and color Cell size and color
varyvary Count Cells only – not Count Cells only – not
light transparent partslight transparent parts Inconsistency in imageInconsistency in image
• BrightnessBrightness• ContrastContrast• Color castColor cast• SharpnessSharpness
Images are uniqueImages are unique Hard to find algorithm Hard to find algorithm
that is compatible with that is compatible with all imagesall images
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AlgorithmAlgorithm
PreprocessingPreprocessing• Separate RGB channels set thresholdsSeparate RGB channels set thresholds
Eliminate background and Villi edgeEliminate background and Villi edge Separate Red and Blue cellsSeparate Red and Blue cells
Count Blue CellsCount Blue Cells• Count # of connected regionCount # of connected region
Calculate PercentageCalculate Percentage• Calculate area of Blue and Red cellsCalculate area of Blue and Red cells
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PreprocessingPreprocessing Transform Transform
(stretch) image (stretch) image • Better contrastBetter contrast
Can separate blue Can separate blue and red cells from and red cells from image using image using Green channelGreen channel• Problem: edgeProblem: edge
Eliminate Eliminate background & background & edgeedge• ~White=> R=B=G~White=> R=B=G• Dilate & Subtract Dilate & Subtract
from original from original imageimage
EDGE
Stretched Background extraction
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PreprocessingPreprocessing Red ExtractionRed Extraction
• Create binary templatesCreate binary templates Red>BlueRed>Blue Red>GreenRed>Green
• Combine binary templatesCombine binary templates• ““And” w/ No-background And” w/ No-background
imageimage
Blue cells
Red cells
Blue ExtractionBlue Extraction• Create binary templatesCreate binary templates
Red<BlueRed<Blue Red<GreenRed<Green
• Combine binary templatesCombine binary templates• ““And” w/ No-background And” w/ No-background
imageimage
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Works on Variety of imagesWorks on Variety of images
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CountingCounting Convert the processed Convert the processed
images into binary images into binary imagesimages
Eliminate small Eliminate small regions and close regions and close small gaps that small gaps that humans cannot humans cannot distinguishdistinguish
Use built-in MATLAB Use built-in MATLAB functions to count the functions to count the area, and the number area, and the number of cellsof cells Area = 9246
Cells = 110
Area = 175018Cells = 390
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Algorithm OverviewAlgorithm Overview
Background Extraction
Binary image
Stretching Transformation
Blue pixels Red pixels
Original Image
Blue Extraction
Red Extraction
Calculate: Cell number Area Percentage
Dilation/Erosion
intersect
intersect
dilate
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Graphical User InterfaceGraphical User Interface User selects Magnification User selects Magnification
of Imageof Image• Different algorithm for Different algorithm for
different magnificationdifferent magnification User selects area of image User selects area of image
or entire image to be or entire image to be processedprocessed
Results are displayed in Results are displayed in graphical formgraphical form
Results include:Results include:• Cell areaCell area• Cell countCell count• PercentagePercentage
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Questions?Questions?