Automation of Vessel Counting Jessica DeQuachBoris Babenko Christman LabBelongie Lab.

Slides:



Advertisements
Similar presentations
Muscle & Nerve Tissues. skeletal muscle, 10X, voluntary, striated attached to bones.
Advertisements

The Human Muscular System
The Muscular System 36-2 BIO 1004 Flora. Types of Muscle Tissue 3 Different Types of muscle tissue: o Skeletal o Smooth o Cardiac o Each type of muscle.
Anatomy Overview THE CIRCULATORY AND LYMPHATIC SYSTEMS.
Dr Azra Parveen Senior Registrar Medicine. Acute myocardial infarction is the rapid development of myocardial necrosis caused by a critical imbalance.
Heart disease. Aim To review cardiac cycle with an exam question To understand how atheroma and thrombosis can lead to heart attacks To learn what an.
Anatomy and Physiology Blood vessels. Blood vessel overview Blood travels from the heart through arteries. Initially these are large and very elastic.
Lab Practical Know the following slides
Daniel et al Suppl. Fig. 1 a b a Co-staining for p-STAT3 and α-smooth muscle actin revealed that p-STAT3 is predominantly expressed in neointimal SMCs.
Muscular System. Three Types Skeletal or striated – attached to bones, allows motion, voluntary control Smooth - work internal systems, involuntary i.
Remodelling Ability of living tissue to adapt to its environment by changing its shape and structure Modifies mechanical properties Driven by tendency.
Muscular System. Facts about muscles… A skeleton cannot move by itself > 40% of the mass of the average human body is muscle Found everywhere in your.
CARDIAC MUSCLES Presented by: Tagreed AL-turki. Contents: different type of muscles Heart structure The wall of the heart Cardiac muscle cell structure.
Structural Complexity in Living Things From Atoms to Organisms.
Date of download: 5/27/2016 Copyright © The American College of Cardiology. All rights reserved. From: Increased myocardial apoptosis in patients with.
Date of download: 6/1/2016 Copyright © The American College of Cardiology. All rights reserved. From: Sonic Hedgehog-Induced Functional Recovery After.
Thrombosis and Embolism. Thrombus Thrombus: a blood clot occurring in a vessel or the heart Thrombus: a blood clot occurring in a vessel or the heart.
Grafting an Acellular 3-Dimensional Collagen Scaffold Onto a Non-transmural Infarcted Myocardium Induces Neo-angiogenesis and Reduces Cardiac Remodeling 
Jonathan Bomar1, Scott Collins Ph.D1,2, and Rosemary Smith Ph.D1,3
Right Ventricular Outflow Tract Repair with a Cardiac Biologic Scaffold Cells Tissues Organs 2012;195:159–170 - DOI: / © 2011 S. Karger.
In Search of the Optimal Set of Indicators when Classifying Histopathological Images Catalin Stoean University of Craiova, Romania
Heart Disease - Atherosclerosis
Do Now: Major Muscles of the Leg
Muscle Tissue Function --- produce movement Three types
In Vivo Cardiac Cellular Reprogramming Efficacy Is Enhanced by Angiogenic Preconditioning of the Infarcted Myocardium With Vascular Endothelial Growth.
Body Organization, Part 1
Right Ventricular Failure in Idiopathic Pulmonary Arterial Hypertension Is Associated With Inefficient Myocardial Oxygen UtilizationClinical Perspective.
Therapeutic angiogenesis using autologous bone marrow stromal cells: improved blood flow in a chronic limb ischemia model  Abdulaziz Al-Khaldi, MD, Hilal.
A combination of omental flap and growth factor therapy induces arteriogenesis and increases myocardial perfusion in chronic myocardial ischemia: Evolving.
Volume 8, Issue 4, Pages (April 2011)
by Simon F. De Meyer, Alexander S. Savchenko, Michael S
VEGF Gene Delivery to Muscle
by Sara M. Weis, Jeffrey N. Lindquist, Leo A. Barnes, Kimberly M
Mesenchymal stem cell implantation in a swine myocardial infarct model: engraftment and functional effects  Jay G. Shake, MD, Peter J. Gruber, MD, PhD,
Transgenic model of cardiac rhabdomyosarcoma formation
Combined transplantation of skeletal myoblasts and angiopoietic progenitor cells reduces infarct size and apoptosis and improves cardiac function in chronic.
Hui-Fang Song et al. BTS 2017;j.jacbts
Long-term patency of small-diameter vascular graft made from fibroin, a silk-based biodegradable material  Soichiro Enomoto, MD, PhD, Makoto Sumi, MD,
Thomas E. Arnold, MD, Dmitri Gnatenko, PhD, Wadie F. Bahou, MD 
Volume 91, Issue 5, Pages (May 2017)
Animal Body Systems: Organization
Murine abdominal aortic aneurysm model by orthotopic allograft transplantation of elastase-treated abdominal aorta  Zhenjie Liu, MD, PhD, Qiwei Wang,
Tissue-engineered pro-angiogenic fibroblast scaffold improves myocardial perfusion and function and limits ventricular remodeling after infarction  J.
Hui-Fang Song et al. BTS 2017;2:
Romain Gallet et al. BTS 2016;1:14-28
EphB4 stimulation prevents aberrant angiogenesis by uncontrolled adenoviral VEGF delivery both in normal and in ischemic muscle EphB4 stimulation prevents.
Jason A. Bartos et al. BTS 2016;j.jacbts
Fig. 6 pDCs infiltrate the skin of BLM-treated mice, and their depletion attenuates skin fibrosis. pDCs infiltrate the skin of BLM-treated mice, and their.
Improvement of cardiac function in the failing rat heart after transfer of skeletal myoblasts engineered to overexpress placental growth factor  Matthias.
Novel regenerative therapy using cell-sheet covered with omentum flap delivers a huge number of cells in a porcine myocardial infarction model  Yasuhiro.
G. Chad Hughes, MD, James E Lowe, MD, Alan P Kypson, MD, James D St
Elysse C. Filipe et al. BTS 2018;3:38-53
Myocardial rescue with autologous mitochondrial transplantation in a porcine model of ischemia/reperfusion  Aditya K. Kaza, MD, Isaac Wamala, MD, Ingeborg.
Improved heart function with myogenesis and angiogenesis after autologous porcine bone marrow stromal cell transplantation  Shinji Tomita, MD, PhD, Donald.
Confocal fluorescence microscopical images of 3-nitrotyrosine-positive blood vessels from a patient with mitochondrial disease. Confocal fluorescence microscopical.
Elysse C. Filipe et al. BTS 2018;3:38-53
Robotic minimally invasive cell transplantation for heart failure
Levels of Structural Organization
Cellular therapy reverses myocardial dysfunction
Volume 19, Issue 4, Pages (April 2011)
Obliteration of pulmonary arteries precedes pulmonary fibrosis in fra-2tg mice. Obliteration of pulmonary arteries precedes pulmonary fibrosis in fra-2tg.
Sebastiano Sciarretta et al. JACC 2018;71:
Elysse C. Filipe et al. BTS 2018;3:38-53
Remodeling and maturation of the mouse retinal vasculature.
Expression of tomoregulin-1 in wild-type and cardiac hypertrophy mouse myocardium. Expression of tomoregulin-1 in wild-type and cardiac hypertrophy mouse.
Muscle Tissue.
Volume 24, Issue 1, Pages (January 2016)
Oxidative stress is elevated in tumors grown in Fbln5−/− mice.
Effect of mitomycin C and bortezomib on the growth of LS174T intraperitoneal tumors. Effect of mitomycin C and bortezomib on the growth of LS174T intraperitoneal.
The Angiogenesis Inhibitor Vasostatin does not Impair Wound Healing at Tumor- Inhibiting Doses  Bernhard Lange-Asschenfeldt, Paula Velasco, Michael Streit,
Presentation transcript:

Automation of Vessel Counting Jessica DeQuachBoris Babenko Christman LabBelongie 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

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

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

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 Quantification Identify injection region 858_82_16

Vessel Quantification Identify injection region 854_123_70

Vessel Quantification Identify injection region 879_192_17

Vessel Quantification Draw long and short axis

Vessel Quantification Not 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 Boris Babenko Anthony Monteforte