Automation of Vessel CountingJessica DeQuach Boris BabenkoChristman Lab Belongie Lab

Heart Attack

Death of cells

Degradation of ECM

Heart Failure

Negative left ventricular remodeling

Wall thinning

Myocardial Infarction and Heart Failure

LV

RV

Myocardial Infarction and Heart Failure

6 weeks later….

Research With Injectable Biomaterials

•Want to develop an injectable biomaterial to help regenerate/salvage damaged tissue▫Skeletal muscle▫Heart

•Injectable materials▫Minimally invasive (less surgery)▫Contours to shape of wound

Animal Surgeries

• Surgeries performed by Pam or Rebecca

• Animals anesthetized▫First surgery: injury

(infarct, ischemia)▫Second surgery:

injection, ~1 week later•Animals kept in

vivarium until time point

http://kentsimmons.uwinnipeg.ca/16cm05/16labman05/lb8pg12.htm

Animal Studies (weeks to months)

• To get statistical significance, usually need n >= 4 per group▫Need to account for animal death, and

variability

• Need to compare to a control group

• Note* need to include different experimental groups on each day

Analysis

•Various methods to determine whether the material is helping the damaged area▫Function

▫Neovascularization▫Wall thickness▫Cellular infiltration

MRI

Neovascularization

•Formation of new blood vessels with red blood perfusion

http://www.omegagenesis.com/html/Research.html

Animal Studies (weeks)

• Harvest tissue, freeze in OCT• Section the sample to 10 um slices

Injection Region

• Identify the injection region• Stain five evenly spaced slides

through the injection region

H&E

Vessel Stain

• Antibody stain for vessels▫Antibodies can identify

specific proteins

•Smooth muscle actin (red)▫Stains for smooth muscle

cells

• Isolectin (green)▫Stains for endothelial cells

http://www.siumed.edu/~dking2/crr/cvguide.htm

Animal Studies (weeks)

• Take images of vessel stain

• Need to quantify!▫The annotator should be trained to

be consistent▫Blinded so that no bias▫Only one person can quantify a set

of data

Vessel Quantification

• Criteria:▫Within infarct or injection region▫Has a lumen▫Average diameter > 10 um

Vessel QuantificationIdentify injection region

858_82_16

Vessel QuantificationIdentify injection region

854_123_70

Vessel QuantificationIdentify injection region

879_192_17

Vessel QuantificationDraw long and short axis

Vessel QuantificationNot all pictures will be that pretty

872_112_21

Vessel Quantification

• Vessel long and short axis are averaged

• Only count vessels > 10 um

• Hundreds of images, takes hours

• Only 1 person can quantify

Automation

• Automation of the process would be beneficial

• Need to determine “human error”

• This is where you come in!

• Quantify 150 images of skeletal muscle and heart. Will need MATLAB, can do this from home

• Need data from several people

Matlab Program (designed by Boris et al)

Computer Vision (Belongie Lab)

•Combination of Artificial Intelligence, Machine Learning, Image Processing, 3D Geometry (and sometimes Cognitive Science)

•Examples in Industry:▫Face detection (i.e. most P&S cameras

today)▫Google Goggles / TinEye

Computer Vision (Belongie Lab)

•Pedestrian Detection

•Reading text “in the wild”

Computer Vision and Bio

•Smart Vivarium (Piotr Dollar et al.)

•Coral Classification (Oscar Beijbom et al.)

Training

•We will first label 10 images together•Then you will label 10 image on your own

▫After someone double checks the answer you will be okay to quantify on your own

Commitment

•Quantify 150 images of cardiac and skeletal muscle, only in the Region of Interest (ROI)

•The Matlab program will automatically save your data even if it crashes

•Can pace yourself, measure 10 or so a day

•Opportunity to participate in Bioengineering Research, and can come to lab meetings, etc.

Contacts

•Jessica DeQuach•jdequach@ucsd.edu

•Boris Babenko•bbabenko@ucsd.edu

•Anthony Monteforte•amontefo@ucsd.edu