Small Intestine Villi Cell Small Intestine Villi Cell Counting Counting

Meghan OlsonMeghan Olson

& &

Jittapat BunnagJittapat Bunnag

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

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

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

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

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

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

Works on Variety of imagesWorks on Variety of images

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

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

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

Questions?Questions?