Post on 04-Jan-2016
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