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Biomedical Informatics 260: Computational Methods for Biomedical Image Analysis and Interpretation (BIOMEDIN 260, RAD 260)

General Course Information

|Overview | Detail | Staff | Video Lectures | Audience | Textbooks

Overview:

Biomedical imaging is an exploding field. The technologies for visualizing the body (the imaging modalities) are becoming very powerful, providing exquisite images of tissue morphology, revealing tissue function, and even beginning to see molecular events such as gene expression. Imaging is at the core of medical practice; nearly all patients have imaging of some sort during care, and many studies produce thousands of images. Just as the genetic data explosion has fueled the field of bioinformatics, the growth in digital imaging is necessitating techniques in imaging informatics.

Imaging Informatics is the science of analytic, storage, retrieval, and interpretive methods to optimally use the increasingly voluminous imaging data in biomedicine, and integrate and understand them in the context of complementary molecular and clinical information to improve clinical diagnosis and therapy in medicine. Imaging informatics spans a broad spectrum of topics that include engineering, computer science, statistics, radiology, and medicine. This course will provide a broad overview this field as well as the foundation techniques required to process, analyze, and use images for scientific discovery and applications.

Topics covered in this course:

  • Types of imaging methods and how they are used in biomedicine
  • Image processing, enhancement, and visualization
  • Computer-assisted detection, diagnosis, and decision support
  • Access and utility of publicly available image data sources
  • Linking imaging data to clinical data and phenotypes
  • Computer reasoning with images
  • New questions in biomedicine using imaging informatics. Case studies.

Detail:

Also known as: Rad 260

Units: 4 (or 3 with consent of instructor)

Lectures: Spring Quarter 2012-2013, Monday and Wednesday 12:50-2:05 PM, Location Gates B03
Map to Gates

Review Section (TA-led): Fridays 1:00-2:15 PM, Location: Alway M212/212A (Fleishman Labs), April 26 in M114

First class: Monday, April 1, 2013

Prerequisites: Programming ability at the level of CS 106A, familiarity with statistics, basic biology, knowledge of Matlab (highly recommended), or approval of the instructor.

Grading: BMI260 Projects (40% total, 10% each), Participation (10%), Midterm (25%), Final Project (25%)

Participation: There are many different ways to participate, including but not limited to attending class, attending section, asking questions, and contributing to Piazza.

Staff:

Instructors:

Part I: David Paik, PhD, Assistant Professor of Radiology Profile | Lab
david.paik@stanford.edu

Part II: Daniel Rubin, MD, MS, Assistant Professor of Radiology Profile | Lab
dlrubin@stanford.edu

Teaching Assistants:

Vanessa Sochat: vsochat@stanford.edu
Rebecca Sawyer: rlsawyer@stanford.edu

Office Hours:

TAs. Vanessa: TBA, Rebecca: TBA
Location: TBA

Professor Rubin: by appointment (email Kelly Englese kenglese@stanford.edu to set up a meeting time). Lucas P285.

Professor Paik: by appointment (email Professor Paik directly, then email Professor Paik first, then Maggie Bos (mobs@stanford.edu) to set up a meeting time). Lucas P287.

Directions to Lucas

Contact/Questions: Most questions should be posted to the Discussions page, so that all students can benefit from the answers. Other queries can be directed to the TA and the professors at:

biomedin260-spr1113-staff@lists.stanford.edu

The professors or TAs will respond as soon as possible.

Audience:

This course is designed for:

• Graduate students in biomedical informatics, computer science, bioengineering, or other related disciplines
• Medical students
• Medical, pediatric, surgical or other fellows with an interest in learning and using imaging informatics in research
• Interested undergraduates
• Auditors welcome including medical staff, medical/pediatric/surgical fellows, post-doctoral fellows, and undergraduates. Please contact us to be added to the class email list.

Video Lectures:

The video lectures can be accessed via SCPD.


Textbooks:

Required books: None (the course will be taught using recent publications)

Recommended books:

• Digital Image Processing in Matlab - Gonzales and Woods Also see here
• Insight into Images-Yoo
• Digital Image Communications in Medicine-Pianykh
• Practical Imaging Informatics-Branstetter
• Naked to the Bone - Bettyann Kevles

Coursework:

Questions

Students should sign up for discussions on Piazza under BIOMEDIN 260. Piazza board
Students who do not possess a @stanford.edu e-mail should contact TAs to be added to the board.

Readings

Readings are linked from each lecture on the Syllabus page. Expect two to three readings per class as preparation.

Software and computing resources:

You may purchase a student license to Matlab. Alternatively, you can use the Leland clusters (cardinal.stanford.edu; Matlab is installed; you must use X-windows server on your local computer).

Collaboration policy:

You can talk with others in the class about the class projects, but you must turn in your own individual work and do the programming yourself.

Due dates:

Projects are due at or before 11:59 PM on the due date. You are allotted 4 free late days total this quarter, so use them wisely for the four problem sets. After that, 20% off your grade per day late. Any late time within a day used will be counted as a full late day. Not using all your late days may influence your final grade (bump up) if borderline.

Course projects

During the quarter, the students will undertake developing and implementing four substantial imaging informatics applications, increasing in difficulty during the quarter.

Midterm Exam

Based on the lectures and the readings. Open book. To be held during class, Wednesday, May 1st.

Final Project Presentations

To be held Wednesday, June 12 from 8:30-11:30 AM.

Honor code

Stanford University's Honor Code will be observed and uphold at all times.

Students with Documented Disabilities

Students who may need an academic accommodation based on the impact of a disability must initiate the request with the Office of Accessible Education (OAE). Professional staff will evaluate the request with required documentation, recommend reasonable accommodations, and prepare an Accommodation Letter for faculty dated in the current quarter in which the request is made. Students should contact the OAE as soon as possible since timely notice is needed to coordinate accommodations. The OAE is located at 563 Salvatierra Walk (phone: 723-1066, URL: http://studentaffairs.stanford.edu/oae.