ImageJ Classes

    Classes and workshops are FREE to anyone interested in image processing with ImageJ. Off-campus visitors are welcome. Our room size is limited so all potential attendees please register with the form below. You will receive an immediate confirmation email followed by a reminder email with digital materials before the class.

    Class companion manuals are available in the ImageJ Tutorials section further down this page.

    Class Schedule Summer 2017

    Summer Session #1 Wednesday June 14th 1:00-3:30pm Cummings 119
    Summer Session #2 Wednesday June 21st 1:00-3:30pm Cummings 119
    Macro Writing Workshop Wednesday June 28th 1:30-3:30pm Cummings 119

    Class Descriptions

    Summer Session Combines ImageJ Basics and Intermediate ImageJ into one class, so you only need to attend one session!

    ImageJ Basics will show you how to get from raw data to a multi-panel, multi-color paper or talk figure. Topics include: opening images from proprietary file types (such as Leica .lif and .lei, SlideBook .sld), creating multi-color images, adding scale bars, working with hyperstacks, and installing and using plugins and macros.

    Intermediate ImageJ builds on the Basics class, covering basic image quantification. Topics include particle counting, intensity analysis, using the ROI manager and basic colocalization with the JACoP plugin.

    For Basics and Intermediate classes, a laptop pre-loaded with ImageJ or Fiji is welcome but NOT required.

    Macro Workshops are for people already doing figure creation and / or image analysis with ImageJ. We will cover macro writing basics and then participants will get a chance to write their own macro (on their own laptop) with help. For Macro Workshops, a laptop with ImageJ or Fiji installed and a few "test" images of the kind you want to process are encouraged. No prior computer programming experience is necessary.

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    ImageJ Macros

    ImageJ is scriptable software! Macros can be used to automate image processing with ImageJ/Fiji. Click here for links to macros developed at the University of Chicago imaging facility.

    In the spirit of open-source software, these macros are free for anyone to use and modify for their own research, but if you do use or modify the code and re-release it into the wild, please acknowledge the macro writer(s).


    Download Sites

    ImageJ Java-based, open source software supported by the NIH. Works on any platform (Windows, Mac, Linux). For more information on how to use ImageJ, see the "ImageJ Tutorials" section below.

    Fiji version of ImageJ (contains a selection of useful plugins and additional features)

    McMaster Biophotonics version of ImageJ by Tony Collins at the McMaster University website.


    ImageJ Tutorials Written by Core Staff

    ImageJ Basics Tutorial (downloadable .pdf) -- Just downloaded ImageJ and wondering what to do next? This is the tutorial for you! It covers basic topics including how to open an image or stack of images, adjusting brightness and contrast, how to make color and multicolor merge images, adding scale bars, and how to make 3D and timelapse movies.

    ImageJ Basics Tutorial, the movie (requires Adobe Flash, may not be compatible with some Mac OS) -- A movie version of Christine's ImageJ Basics Tutorial. Winner of the ImageJ User and Developer Conference 2008 Video Tutorial Competition.

    ImageJ Intermediate Class Tutorial (downloadable .pdf) -- The companion to our Intermediate ImageJ class. Contains information on image quantification, including object counting, area / length / intensity measurements and use of the Redirect and ROI manager tools.

    ImageJ Macro Writing Workshop (downloadable .pdf) -- The Power Point from our Macro Writing Workshop. Contains tips for macro writing / troubleshooting illustrated with sample code

    Download-able tutorial .pdfs for more advanced ImageJ functions:

    Converting Pannoramic Viewer files to open in ImageJ

    Opening files with the LOCI Bio-Formats plugin

    Merging colors beyond RGB

    Making montages

    Basic cell counting

    Counting objects by template matching


    ImageJ Books and Other Resources

    Digital Image Processing, An Algorithmic Introduction Using Java by Wilhelm Buger and Mark Burge. A classic book on digital image processing. Uses ImageJ as its main image processing sofware.

    Image Processing with ImageJ by Javier Pascau and Jose Maria Mateos Perez. Available in paper and digital forms, this is a wonderful introduction to all aspects of ImageJ. Covers program installation, opening images, filtering, image cleanup, object counting, macro writing and many other topics.

    ImageJ User Guide by Tiago Ferreira and Wayne Rasband. The definitive guide to all things ImageJ and Fiji. Written by the creator of the original NIH Image and ImageJ source code.

    Links to additional ImageJ tutorials and documentation can be found on the ImageJ documentation page.