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Automation of Vessel Counting

Automation of Vessel Counting. Jessica DeQuach Boris Babenko Christman Lab Belongie Lab. Death of cells. Degradation of ECM. Wall thinning. Negative left ventricular remodeling. Heart Failure. Myocardial Infarction and Heart Failure. Heart Attack.

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Automation of Vessel Counting

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  1. Automation of Vessel Counting Jessica DeQuach Boris Babenko Christman Lab Belongie Lab

  2. Death of cells Degradation of ECM Wall thinning Negative left ventricular remodeling Heart Failure Myocardial Infarction and Heart Failure Heart Attack

  3. Myocardial Infarction and Heart Failure RV LV 6 weeks later….

  4. 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

  5. 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

  6. 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

  7. Analysis • Various methods to determine whether the material is helping the damaged area • Function • Neovascularization • Wall thickness • Cellular infiltration MRI

  8. Neovascularization • Formation of new blood vessels with red blood perfusion http://www.omegagenesis.com/html/Research.html

  9. Animal Studies (weeks) • Harvest tissue, freeze in OCT • Section the sample to 10 um slices

  10. Injection Region • Identify the injection region • Stain five evenly spaced slides through the injection region H&E

  11. 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

  12. 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

  13. Vessel Quantification • Criteria: • Within infarct or injection region • Has a lumen • Average diameter > 10 um

  14. Vessel Quantification Identify injection region 858_82_16

  15. Vessel Quantification Identify injection region 854_123_70

  16. Vessel Quantification Identify injection region 879_192_17

  17. Vessel Quantification Draw long and short axis

  18. Vessel Quantification Not all pictures will be that pretty 872_112_21

  19. Vessel Quantification • Vessel long and short axis are averaged • Only count vessels > 10 um • Hundreds of images, takes hours • Only 1 person can quantify

  20. 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

  21. Matlab Program (designed by Boris et al)

  22. 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

  23. Computer Vision (Belongie Lab) • Pedestrian Detection • Reading text “in the wild”

  24. Computer Vision and Bio • Smart Vivarium(Piotr Dollar et al.) • Coral Classification (Oscar Beijbom et al.)

  25. 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

  26. 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.

  27. Contacts • Jessica DeQuach • jdequach@ucsd.edu • Boris Babenko • bbabenko@ucsd.edu • Anthony Monteforte • amontefo@ucsd.edu

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