Automatic Cell Counting

Ege EnginMiddle East Technical University

Supervisor: Tomas LukesCzech Technical University

http:/blog.metu.edu.tr/e174088

Agenda

• Introduction

• Different Approaches• Method 1• Method 2• Method 3

• Comparison & Results & Comments

• Nine-Point Circle for Cell Segmentation• Nine-Point Circle Rule• How to use?• Results• Implementation

• Conclusion and further work

Background

• Learn image processing basics

• Fundamentals

• Intensity Transforms

• Spatial Filtering

• Frequency Domain Processing

• Image Segmentation

• Implement different methods in MATLAB and compare them

• Based on the results, improve the algorithm

1st and 2nd Method

1st Method

• Thresholding:• im2bw with graythresh

• Filling with holes• imfill with holes

• Counting:• Numobjects of

bwconncomp

2nd Method

• Thresholding:• im2bw with graythresh

• Filling with holes• imfill with holes

• Counting:• Lenght of bwboundaries

3rd Method

3rd Method• Image: Cell 1

Comparison & Results1st Method

2nd Method

3rd Method

3rd Method( with watershed)

Exact Number(includes incomplete objects)

Coins 10 37 10 12 10

Eight 1 263 4 3 4

Rice 151 158 93 67 101

Cell Image 1 36 518 53 42 50

Cell Image 2 270 2369 50 44 38

Cell Image 3 287 1139 25 75 64

• Cell Image 2• Cell Image 1 • Cell Image 3

Comments• First two approaches uses nearly the same algorithm except their

counting methods.

• The first algorithm underestimate the number of objects.

• The second algorithm overestimate the number of objects.

• 3rd approach :

• Without watershed segmentation has achieved promising results when the cells in the image are not connected.

• With watershed segmentation over-segments or mis-segments the figure, so overestimate the number of objects.

• Challenges: connected cells, incomplete cells on the borders

• Another solution technique can be useful for the solution of connected cells problem.

Nine-Point Circle • Also known as the Feuerbach Circle

• In every triangle, lie on a circle:

• The three midpoints of the sides

• The three base points(feet) of the altitudes

• The midpoints of the three segments from the orthocenter to the vertices

Reference: Dorrie, H. and Woltermann, M, '100 Great Problems of Elementary Mathematics', reworked in 2010

How to use?• Arbitrarily select three points from cell

• Example: A,B,C

• Find 9 points which are• 3 midpoints

• Example: D,E,F

• 3 base points(feet) of the altitudes• Example: G,H,I

• Midpoints of 3 segments from the orthocenter to the vertices

• Example: K,L,M• Please note that: J is orthocenter.

• Count the points inside the cell:• D,E,G,K,L,M => 6 inside / 9 total

• Repeat the procedure until the average is an appropriate result

Results• For Results:

• For Implementation:

Conclusion• When useful?

• When cells have circular shapes

• Why?

• The more circular the shape, higher the average algorithm givesso,When the cells are not connected, the average will be higher.

• Can help to distinguish the cells whether connected or not.

• Why important?

• For cell segmentation, not tried before ( based on subjective(my) research)

• Challanges?

• Defining the standard to understand whether cells are connected

• Clear bordering is necessary to run correctly

• Hard to distinguish if cells are connected circularly

Future Study

• For nine-point rule cell segmentation:

• Divide the given image in appropriate divisions

• Try on cell images

• Documentation related to all studies

Questions

Reference: Velasquez J., Dhuru P. & Vaghani M. , ‘Matlab Digital Image Processing For Microscopy Screening’

Thank you!

Reference: A blood test and examination, 1941 – 1945 retrieved byhttp://research.archives.gov/description/513715 on 20.08.2013

3rd Method

3rd Method

3rd Method