Key Information:

  • Location: Online via Zoom
  • Course Dates:August 17-21st
  • Application deadline: July 18st (11:59PM PDT)
  • Course Website: https://SlicerMorph.github.io/2020_Summer_Workshop
  • Admission notification: August 1st
  • Course Flyer & Tentative Schedule(PDF)

  • Target Audience: Course is directed for students, post-docs and junior faculty who are interested in conducting quantitative research into organismal form and function using 3D imaging. It is also appropriate for more established researchers who are looking for open-source alternatives to the proprietary pipelines they have been using. We anticipate more applicants than we can accommodate. Applicants whose host institution lack such curriculum and/or resources might be given preference.

    Course Contents and Structure: Due to change to online format and with shortened hours, course will prioritize hands-on contents and computer labs over formal didactics. Labs will cover all aspects of conducting specimen-based research using 3D imaging. Practical topics (e.g., image processing and segmentation, visualization) will be taught using the open-source 3D-Slicer visualization suite and the SlicerMorph morphometrics toolkit (statistical shape analysis) Additional lab topics include using 3D specimen repositories to obtain data, tools and methods for collaboration and reproducible research, introduction to data analysis through R/Python. Course material will be focused on volumetric (e.g., CT or microCT) 3D datasets, but will be equally applicable to data from 3D surface scanners.

    Expectations from attendees: Each attendee should have a recent (last two years) laptop running Windows, Mac or Linux OSes (no netbooks or tablets). More information about computer requirements and how to obtain the course software can be found at here.

    Logistics: Selected applicants will be notified by August 1st. Due to demand and limited number of participants we can accommodate online, we will prioritize applicants who can attend the whole session. Each day will start at 9.30 (PDT) and end around 2p (PDT) with a 20 minute break sometime in between sessions.

    Course FeeThere is no course registration fee. This workshop and SlicerMorph project are supported by a collaborative research grant from the National Science Foundation Advances in Biological Informatics program (ABI-1759637, Adam Summers & Murat Maga).

    Contact information: If you have any questions, please email us at SlicerMorph@outlook.com, and one of the course directors will respond to you inquiry.

    Ready to apply? Submit your application. Please be prepared to give a short description of your research background, your career goals as they apply to this workshop, and a working email address. Email is the primary mean we will be contacting you, so please make sure to enter correctly.