detection of cell mitosis for population growth analysis n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Detection of Cell Mitosis for Population Growth Analysis PowerPoint Presentation
Download Presentation
Detection of Cell Mitosis for Population Growth Analysis

Loading in 2 Seconds...

play fullscreen
1 / 13

Detection of Cell Mitosis for Population Growth Analysis - PowerPoint PPT Presentation


  • 175 Views
  • Uploaded on

Detection of Cell Mitosis for Population Growth Analysis. Kyri Baker Carnegie Mellon University Methods in Medical Image Analysis Spring 2010. Outline. Objective/goal of this project Motivation Steps to achieve this goal and difficulties encountered Results and other methods Questions.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Detection of Cell Mitosis for Population Growth Analysis' - brenna


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
detection of cell mitosis for population growth analysis

Detection of Cell Mitosis for Population Growth Analysis

Kyri Baker

Carnegie Mellon University

Methods in Medical Image Analysis

Spring 2010

Kyri Baker 2010

outline
Outline
  • Objective/goal of this project
  • Motivation
  • Steps to achieve this goal and difficulties encountered
  • Results and other methods
  • Questions

Kyri Baker 2010

objective
Objective
  • Detect stem cell mitosis (divisions)
  • Automatically monitor how cell population changes over time when injected with a growth hormone

Mitotic Event: Cell brightens, enlarges, and divides

Kyri Baker 2010

motivation
Motivation
  • Want to farm stem cells for use in tissue regeneration
  • Biologists culture groups of cells and monitor how they react to specific growth hormones
  • A sign of a good growth hormone is one that causes the lineage tree to be symmetric

Mitosis

Cell Lineage Tree

Mitosis

Kyri Baker 2010

the data
The Data
  • Hematopoietic stem cells from the bone marrow of adults
  • Dosed with a growth drug and chemicals to prevent clumping
  • Imaged every 30 seconds ≈ 11,000 frames

Frame 1 Frame 11,000

Kyri Baker 2010

how to detect mitosis
How to Detect Mitosis?
  • Many techniques can be experimented with

- In general, cells become brighter and rounder

- But illumination conditions can change, other cells can also be round

  • For certain: Cell area increases because another cell is being “born”!

 Meat of the algorithm: Monitor overall cell areas over time, and when the area of a cell starts to increase, mitosis is happening

 Challenge: How to accurately find the cell areas?

Kyri Baker 2010

step 1 preprocess image
Step 1: Preprocess Image

1. Import Image

2. Threshold Image

3. Apply Hough Transform for circle

detection

4. Set all pixels outside detected

circle to black

Kyri Baker 2010

step 2 correlation filter
Step 2: Correlation Filter
  • To refine the boundaries of cell nucleus and cell membrane
  • Used itkNormalizedCorrelationImageFilterwith an annulus mask
  • Cannot correlate with a template like:

- Cells touching looks like mitosis:

Mitosis Frames after Correlation Filter

Kyri Baker 2010

step 3 watershed image filter
Step 3: Watershed Image Filter
  • Find the areas of different cells

Mitotic Cell Non-Mitotic Cells

Larger Area

Mitotic Cell

Difficulties:False positives from image noise

Nucleus Area ≈ 90-120

Nucleus Area ≈ 60-90

Kyri Baker 2010

mini steps relabeler colorfilter
Mini Steps: Relabeler, ColorFilter
  • Order watershed areas from largest to smallest with itk::RelabelComponentImageFilter
  • For nice watershed output visualization used itk::Functor::ScalarToRGBPixelFunctor

Kyri Baker 2010

results
Results

Actual Mitosis

Algorithm Detected Mitosis

Number of

Mitotic Cells

Frame

  • Current best results were achieved with:
  • Lower intensity threshold = 120
  • Taking watershed regions with area > 120 pixels
  • Only keep as a true “mitotic event” if mitosis was detected over a series of 3 frames
  • or more

Kyri Baker 2010

other methods attempted
Other Methods Attempted
  • Subtracting previous frame to determine cell growth
    • Cells moved around too much, too many false positives
  • Monitoring overall summed area of all cells
    • Overall area calculation fluctuated too greatly, cannot determine exact instant of mitosis

Overall Cell

Area

Frame

Kyri Baker 2010

questions
Questions?

Kyri Baker 2010