Principles of Microscopy and Image Analysis

LMCF periodically offers a week long class covering a broad range of principles of microscopy and image processing, visualization and analysis. The class will be held each morning for five consecutive days. The next class date is TBA.

The first three mornings will cover how microscopes, confocals and other imaging modalities work - the aim is for you to gain understanding to the level were you are able to choose the best approach for the imaging you want to do and carry out the imaging in the optimal way.

The last two mornings will be interactive image processing and analysis exercises using your own computers. Background will be presented so you gain a thorough understanding of important areas such as bit-depth, digital scaling and contrast, color display, 3D images and visualization and quantification of images.

The course . . .

  • Is open to everybody at Duke (you don't have to be a student)
  • Aimed at people doing some microscopy and wanting to learn more
  • Free!
  • Carries no credit as it is not an official Duke class
  • Has no practical content. If you want to learn how to use a particular microscope in the Light Microscopy Core Facility you can request training here.
  • Requires you to bring a computer with FIJI/ImageJ installed
  • Not trivially easy - expect an introduction to some important concepts and technical details
  • Limited to 20 people

How is this class different to other courses offered by LMCF? It is less detailed than Biology 725 and similar to the CMB 551 module. These are essentially only open to graduate students so this class aims to offer something similar to post-docs, technicians, research associates and faculty. The last two mornings are similar to the image analysis course.

Monday Tuesday Wednesday Thursday Friday
9:30 - 11:30 9:30 - 11:30 9:30 - 11:30 9:30 - 12:30 9:30 - 12:30
  • Fluorescence imaging
  • Optical principles
  • Objectives
  • Transmitted light
  • DIC and phase contrast
  • Optical sectioning
  • Confocal
  • Multiphoton
  • Spinning disk
  • TIRF
  • Sample preparation
  • Live cell imaging
  • Imaging techniques
  • Future methods
  • Digital image fundamentals
  • Bit-depth and grey-values
  • Color
  • 3D images
  • Image processing
  • Image quantification
  • Counting
  • Thresholding and segmentation
  • Colocalization
Slides Slides Slides Slides | Images | FIJI