Microscopy Learning and Workshops

Interactive workshops held each semester are designed for students, post-docs, staff, and faculty to learn about key concepts in imaging, image analysis, or sample preparation.

Workshops on Imaging, Image Analysis, and Sample Preparation for Imaging

Key Concepts in Microscopic Optical Imaging (IAC01)

Summary: An overview of the optical principles behind how common light and electron microscope designs create an image. Intended for researchers who often use microscopes and would like to understand the physical principles behind how microscopes work so that they can use them more efficiently and effectively. No prior knowledge of imaging is required. Time commitment: 8 hours. Offered once per year. Cost: $80.

Main Topics:

  • Conceptual overview of ray optics
  • Conceptual overview of wave optics
  • Optical properties of biological materials
  • Image formation in wide-field microscopes (LM and EM)
  • Image formation in point-scanning microscopes (LM and EM)
  • Overview of super-resolution microscopy
  • Overview of light-sheet microscopy

Slides: Part I: Basic Optics, Part II: Transmitted Techniques, Part III: Fluorescence Microscopy.

Next Offering: TBA

Quick Start Guide to Using FIJI and FluoRender for Visualizing Fluorescence Images (IAN01)

Summary: A practical, basic, and interactive introduction to how to use FIJI and FluoRender freeware for common image visualization and rendering tasks. Attendees should bring a laptop to work along with the examples. No prior knowledge is required. Time commitment: 4 hours. Offered twice each semester. Cost: Free.

Main Topics:

  • Basic introduction to using FIJI and FluoRender
  • Understanding image file types and data types
  • Display and manipulation of 2D images
  • Display of 3D images
  • Interactive rendering of 3D images and 3D movie making

Slides: FIJI Quick Start

Next Offering: TBA

Key Concepts in Image Processing and Analysis (IAN02)

Summary: A conceptually-oriented introduction to the theory behind how many commonly used image processing and analysis methods work. Application examples are demonstrated using FIJI software. Attendees should bring a laptop to work along with the examples. Intended for researchers who would like to learn how to successfully develop workflows to quantify their images in some way. Basic knowledge of FIJI is assumed (e.g. IAN01). Time commitment: 8 hours.Offered once per semester. Cost: $80.

Main Topics:

  • Conversion of analog to digital signals
  • Signal to noise ratio
  • Convolution-based filtering
  • Image registration
  • Correcting for artifactual intensity changes
  • Segmentation approaches
  • Particle Tracking
  • Quantifying cross-channel relationships (ratio images, FRET, colocalization methods)

Next Offering: TBA

Automating and Extending FIJI with Macros (IAN03)

Summary: An interactive introduction on how to automate image processing and analysis using the FIJI macro language. Attendees are asked to bring a laptop to work along with the examples. Basic experience using FIJI (e.g. IAN01) or exposure to a computer programming language is beneficial but not required. Time commitment: 2 hours. Offered once per semester. Cost: $20.

Main Topics:

  • Using the Macro Recorder
  • Overview of macro language syntax
  • Overview of macro language functions
  • Basic programming application examples

Slides: FIJI Macro Workshop

Next Offering: TBA

Advanced Quantitative Methods in Image Processing (IAN04)

Summary:Technical and in-depth lectures on the theory and implementation of select advanced image processing methods. Application examples will be demonstrated using FIJI software. Intended for researchers who use advanced fluorescence imaging methods as a central tool. Familiarity with the optical point spread function, trigonometric functions, and basic statistics is assumed (but will be reviewed). Time commitment: 4 hours. Offered once each year. Cost: $40.

Main Topics:

  • Statistical treatment of noise and de-noising
  • Fourier Transform and Discrete Cosine Transform with applications
  • Power spectra applications
  • Fourier Convolution and Shift Theorems with applications
  • Nyquist Sampling Theorem with compression applications
  • Deconvolution methods (Wiener, Richardson-Lucy, regularization)

Next Offering: TBA

Concepts and Rationales in Sample Preparation for Microscopy (SP01)

Summary: Lectures focused on the rationale behind methods commonly used to prepare samples for microscopic imaging. Will help researchers understand why common protocols work (and sometimes do not work). No prior knowledge required but experience using at least some of the methods discussed is beneficial. Time commitment: 4 hours. Offered once each year. Cost: Free.

Main Topics:

  • Theory and artifacts of fixation
  • Sample prep methods for TEM
  • Sample preps methods for SEM
  • Immunostaining considerations
  • Mounting for light microscopy
  • Tissue clearing
  • Expansion Microscopy
  • How to choose good probes
  • Considerations for live cell imaging

Next Offering: TBA

Past Guest Lectures

Microscopy Core staff are more than happy to contribute graduate-level guest lectures on topics related to imaging, image analysis, or sample preparation for courses or symposia across the university. Past events to which we have contributed to include:

Other Outreach

In addition to educational workshops, we also provide:

  • System repair:  We can provide fee-for-service maintenance on most microscope systems and repair or moving services on systems that are not  under service contract.
  • Microscopes for sale: We occasionally used sell microscopes or parts (e.g. lasers) that work but are no longer of use to the core. Please contact us if you may be interested in purchasing a system or component.
  • Image Analysis: We are happy to help with image analysis on data sets that were not acquired at the core.