Monday, Tuesday, Wednesday, and Thursday, 1 pm to 3 or 4 pm. (See Course Schedule for details)

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Anatomy 6201 Course Director: Dr. Ernesto Phone: (303) 724-3430 Office: RC1 South Rm 11124 Office Hours: by appointment Email: ernesto.salcedo@ucdenver Location ED 2 South Room 2206.

1 Anatomy 6201 Course Director: Dr. Ernesto Phone: (303) Office: RC1 South Rm Office Hours: by appointment Location ED 2 South Room 2206.! Course Hours Monday, Tuesday, Wednesday, and Thursday, 1 pm to 3 or 4 pm. (See Course Schedule for details) Computer Usage Computers will frequently be used for demonstrations, lab, and homework problems. Don t forget to bring your laptops to class! Check your daily for important notices about this course Recommended Book Fundamentals of Medical Imaging. Second Edition. Paul Suetens. ISBN Course Description In this course, we will cover the basic properties of digital images, the techniques used to acquire and process images, and the informatics used to analyze images. We will also explore several different imaging modalities that are commonly used for clinical diagnostics, and explore image datasets derived from these different modalities. Finally, we will introduce some of the methods used to extract digital cross-sections from 3D dimensional datasets. GOALS By the end of this course, you should be comfortable using imaging software, such as the open source software, FIJI, to manipulate and explore the properties of digital images obtained from any of the core imaging modalities discussed in the course, including digital photography, digital microscopy, radiography, magnetic resonance imaging, and sonography. You should also understand the fundamental differences in the properties of images obtained from these core modalities (e.g. resolution or format). Overall Learning Objectives By the end of this course, you should be able to: Define and describe what exactly a digital image is Given an image, find and list its properties such as resolution, size, format, etc. Given an RGB image, create a grayscale image from each of its component channels. Or vice versa, create an RGB from three grayscale images. Create an image with a purple channel (instead of a red one) Given an image, modify its brightness and contrast, extract the histogram, or apply a filter List at least three different image file formats. Understand their strengths and weaknesses Know how to open and manipulate a DICOMM image. Know how to extract a slice from an image stack Describe the methods used to generate the Visible Human dataset. Describe the technique. Describe the resolution of Visible human. Understand how didactic lessons for the Dissector are created Understand the signal-to-noise ratio as it applies to all of the different imaging modalities covered in the course Know the imaging resolutions ranges of a micrograph, a radiograph, an MRI image, and a sonogram. Know what tissue each imaging modality is (and isn t) able to image. Understand how the physics used in each modality affects the quality and appearance of the image Digital Imaging and Modeling I - Fall

2 Read and compare a micrograph, radiograph, MRI image, or sonograph, and describe the anatomical components visible in each image EVALUATION Grades A - 90 to 100% B - 80 to 89.9% C 70 to 79.9% D 60 to 69.9% F - Less than 60% The MSMHA program does not allow for +/- grades Assessment for the course will be the following: Homework assignments and Online Quizzes* 33% * Must be completed on the listed due date prior to the start of class Project proposal 33% Project Presentation 33% Course Project Presentations For your presentations, you will produce both a five- and a ten-minute presentation and discuss the anatomical characteristics of the organ from the microscopic to the macroscopic scale. This presentation should discuss any variabilities seen in the image quality across the modalities and the technical and anatomical reasons behind these variations. In addition to a powerpoint presentation, your final presentation should include some activity that requires audience participation and/or use of the white board. Learning Objectives for this Project include your ability to: Generate and give both a five and ten minute presentation Handle answering questions Authoritatively describe your organ system in a presentation format Compile digital images that will be used in the discussion of your organ system Make measurements of your organ from different imaging modality datasets, including the c/t scans of the cadavers and the visible human dissector Extract image slices from a 3D dataset such as your cadaver ct scan Discuss how the physics of the major imaging modalities (microscopy, radiography, magnetic resonance, and sonography) will affect the image properties of your organ The presentations should follow the following format: Proposal: A five-eight minute didactic presentation that describes your assigned organ and outlines your proposed image analysis project. Your proposal should include: Introduction an overall description of the organ (including ranges in size and weight) Organ function Histological overview of the organ (what cells are typically found in the organ) Any other pertinent information. Image Analysis Proposal should cover the following topics Detail what measurements you will make in your tissue dataset Digital Imaging and Modeling I - Fall

3 Detail what types of variability in anatomy that you will look for you in your c/t cadaver dataset and/or the visible human dataset. Detail what possible anatomical changes can be seen after a pathological state or traumatic episode Final Project: A ten-twelve minute didactic presentation that describes your assigned organ and outlines your image analysis project. Your project should include:! Introduction: a more polished version from the original proposal Detailed Characterization of your organ tissue across the various imaging modalities discussed in the course. This should include: Images curated from various sources including the visible human dissector, the c/t dataset of your cadaver, the images you were able to obtain during gross anatomy, and images from clinical or anatomical studies of your organ. Make sure to cite sources where you obtain your images. At minimum, this should include images from: Histological samples. A radiograph An MRI scan A sonograph. If an image is not available for a given imaging modality, detail why Measurements of your organ using the c/t scan dataset from the three different cadavers and from the visible human dataset. Make sure to list both the mean and the standard deviations in your measurements. Explain possible reasons why these measurements may vary across imaging modalities. Bonus points if you include a discussion from a clinical or anatomical study (from a peer reviewed journal) that is relevant to your discussion. Discussion Course Lecturers Detail any pathology or trauma discovered in your tissue set. If there is no pathology or trauma, detail what level of difference you see in the your organ dataset across the various image modalities. Detail what can and cannot be seen of your tissue organ across the various imaging modalities. Detail how the image of your assigned organ varies in the different imaging modalities (e.g. what can you see using a sonography, a radiography, or MRI) Be specific about when and why you use each modality. This should depend on the goal of the imaging. Notes: Try to treat this talk as a case study. You have been given the ct-scans from three Cadavers. Your goal is demonstrate the usefulness (or lack thereof) of such dataset for dissection. Moreover, these are cadaver datasets. How do they compare to living ct-scans. At there evident differences? Elizabeth Gould, BS Adam Kesner, PhD Stephanie Meyer, PhD elizabeth.gould@ucdenver.edu adam.kesner@ucdenver.edu stephanie.meyer@ucdenver.edu Digital Imaging and Modeling I - Fall

4 Ernesto, MD Jamaluddin Moloo, MD Robert Quaife, MD Charles Ray, MD Michael Silosky, MS Ann Scherzinger, PhD: Vic Spitzer, PhD! Digital Imaging and Modeling I - Fall

5 Course Schedule Subject to change at the Course Director s discretion. NOTE: Classes will be held in ED 2 South, Rm 2206, unless otherwise noted Week Room Date Da y Start End Topic Faculty ONE RC1S /23 W 1:00 3:00 ED 2 S /24 W 1:00 2:00 ED 2 S /24 R 2:00 3:00 Course Overview Light and Vision Vision and Digital Photography Digital Images and Formats TWO 10/28 M Homework/Quiz due ED 2 S /28 M 1:00 1:30 ED 2 S /28 M 1:30 3:00 Fiji: Exploring Digital Image Properties ED 2 S /29 T 1:00 3:00 Generate Figures RC1S /30 W 1:00 4:00 ED 2 S /31 R 1:00 4:00 LAB: Giving Digital Presentations LAB: Photography Lab THREE 11/4 M Homework/Quiz due ED 2 S /4 M 1:00 1:30 ED 2 S /4 M 1:30 3:00 Light Microscopy / Gould ED 2 S /5 T 1:00 3:00 ED 2 S /6 W 1:00 4:00 PMT, Confocal Microscopy, EM Imaging LAB: Digital Photomicrography / Meyer / Gould Ed 2 North P /7 R 1:00 4:00 LAB: Virtual Slides FOUR 11/11 M Homework/Quiz due 11/11 M 1:30 3:00 Open: prepare presentations You Digital Imaging and Modeling I - Fall

6 Week Room Date Da y Start End Topic Faculty ED 2 S /12 T 1:00 3:00 Visible Human Spitzer ED 2 S /13 W 1:00 4: /14 R 1:00 4:00 LAB: Using the Visible Human Dissector Project Proposal Presentations Spitzer You FIVE 11/18 M Homework/ Quiz due ED 2 S /18 M 1:00 1:30 ED 2 S /18 M 1:30 3:00 Introduction to Radiography Silosky ED 2 S /19 T 1:00 2:00 Cardiac C/T Moloo ED 2 S /19 T 2:00 3:00 ED 2 S /20 W 1:00 4:00 ED 2 S /21 R 1:00 4:00 "Clinical Applications of Diagnostic and Interventional Radiology" LAB: Exploring Radiography Datasets Osirix and your CT dataset Ray Scherzinger Lawson SIX 11/25 M Homework/ Quiz due ED 2 S /25 M 1:00 1:30 ED 2 S /25 M 1:30 3:00 General Sonography Scherzinger ED 2 S /25 M 3:00 4:00 MRI Cardiology Quaife ED 2 S /26 T 1:00 3:00 LAB: Ultrasound Scherzinger ED 2 S /27 W 1:00 4:00 11/28 R Nuclear Medicine and PET, PET images No Class - Thanksgiving Adam Kesner SE7EN 12/2 M Homework/ Quiz due ED 2 S /2 M 1:00 1:30 ED 2 S /2 M 1:30 3:00 Sonography - Echocardiology, MD ED 2 S /3 T 1:00 3:00 Intro to MRI Mark Brown Digital Imaging and Modeling I - Fall

7 Week Room Date Da y Start End Topic Faculty ED 2 S /4 W 1:00 4:00 TBD 12/5 R 1:00 4:00 EIGHT 12/9 M 1:00 2:00 ED 2 S /9 M 1:00 1:30 LAB: Exploring MRI dataset LAB: Cardiac Mannequin Homework/ Quiz #7 due Mark Brown, MD ED 2 S /9 M 1:30 3:00 Project preparation /11 W 1:00 4:00 Project Presentations You /12 R 1:00 4:00 Project Presentations You Digital Imaging and Modeling I - Fall

Visualisation : Lecture 1. So what is visualisation? Visualisation

Visualisation : Lecture 1. So what is visualisation? Visualisation So what is visualisation? UG4 / M.Sc. Course 2006 toby.breckon@ed.ac.uk Computer Vision Lab. Institute for Perception, Action & Behaviour Introducing 1 Application of interactive 3D computer graphics to