Workshops & Webinars

As part of our ongoing commitment to the University of Minnesota research community and external investigators, the University Imaging Centers hosts technical workshops for hands-on training, as well as webinars featuring content tailored to our users' needs. 

MSI X501 - Image Analysis Workshop: Analyzing Fluorescence Microscopy Images in FIJI

Date: August 12th, 2024

Registration is open! In this workshop we will go over the basics of working with digital images including noise reduction, segmentation, and automation, with an emphasis on working with microscopy data.

Learners will be using FIJI/ImageJ and should bring a laptop to participate in the workshop. No previous programming experience is necessary. There is a $19.00 registration fee to attend this workshop. Lunch will be provided.

Click here to register!

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Past Workshops

Title Attendees Date(s)
Confocal Workshop (SH) 9 July 6-8, 2022
UIC Multiplexed Ion Beam Imaging (MIBI) Workshop 43 June 29-30, 2022
Segmentation Workflows with FIJI 11 March 25, 2022
Segmentation Workflows with FIJI 13 March 23, 2022
Confocal Workshop (JH) 10  November 2-4, 2021
Confocal Workshop (JH) 15 October 12-14, 2021 
Midwest Association of Core Directors (MWACD) (TCF Bank Stadium) 150 October 16-18, 2019
UIC Nikon SoRa Workshop (CCRB) 30 October 16, 2019
Confocal Workshop (JH) 11  July 16-18, 2019
Confocal Workshop (JH) 12  Jun 18-20, 2019
Live Animal Image Acquisition and Analysis Workshop (JH) 4 April 10, 2019
Confocal Workshop (JH) 10 July 11-13, 2017
Confocal Workshop (JH) 10 June 6-8, 2017
Live Cell Workshop (CCRB) 8 March 8-9, 2017
Confocal Workshop (SH) 5 December 13-15, 2016
UIC & UMII Image Analysis Workshop (CCRB) 15 December 1, 2016
Confocal Workshop (CCRB) 9 November 1-3, 2016
Confocal Workshop (JH) 24 May 17-19, 2016
UIC & UMII Workshop: An Introduction to Image Analysis (CCRB)  21 October 23, 2015
UIC & UMII Workshop: A Hands-On Introduction to FIJI (SH) 13 August 5, 2015
UIC & UMII Workshop: A Hands-On Introduction to FIJI (SH) 18 July 29, 2015
UIC & UMII Workshop: A Hands-On Introduction to FIJI (SH) 15 July 22, 2015

Past Webinar Presentations

Ethical Manipulation of Scientific Images

Digital images are a key tool in biomedical research, allowing fast, unbiased, and reproducible quantification. At the same time, improper manipulations of digital images (accidental or intentional) are a serious threat to the rigor and reproducibility of scientific research. Furthermore, high-profile cases of fraudulent image manipulation seriously damage the public trust in scientific research. This presentation will cover the nature of a digital image, the basic dos and don'ts of digital image manipulation, and some strategies to ensure the integrity of scientific imaging data.

Quantifying Colocalization with FIJI

Colocalization analysis reveals whether two objects occupy the same space at your optical resolution. There are numerous coefficients that calculate the proportion of two signals overlapping with each other (Manders), whether the intensity distributions are correlated (Pearson’s), and the same correlation can also be calculated with ranked pixel intensities as well (Spearman’s).

Spatial analyses measure the proximities of two different sets of labeled objects. These can all be calculated with certain plugins written for the open-source software FIJI.

In this webinar, we’ll review certain principles of colocalization as well as calculate colocalization with the JACoP plugin and perform spatial analysis with the DiAna plugin.

Getting the best from your animal imaging in the UIC Spectrum and IVIS 100 imagers

The purpose of this webinar is to refresh the principles behind the operation of the IVIS bioluminescence and fluorescence animal imagers, as well as the practical aspects of image acquisition. We will cover:

  • Measuring light: calibrated sources
  • The challenges of deep imaging
  • Quantification versus estimation
  • Instrument limitations
  • Step-by-step procedure: dos and don’ts

 

Tissue Clearing and Imaging Services at the University Imaging Centers

This week in the UIC Webinar we will cover the tissue clearing and imaging services at the University Imaging Centers. We will delve into the tissue clearing methods we use as well as our imaging equipment and its capabilities. Our imaging systems are capable of rapid image acquisition in 3D allowing for the assembly of image volumes of samples ranging from sections to intact cubic centimeter volumes of tissues at cellular resolution.

Digital Image Analysis

  • What is a digital image?
  • File saving and archival data storage: Dos and Don’ts
  • Image manipulation: data integrity and reproducibility
  • Processing and restoration
  • Display
  • Analysis (e.g. signal quantification, particle tracking 2D, 3D, spatial relationships in 3D)

 

Reproducibility in Scientific Research: Reporting of Imaging Experiments

In order to replicate an imaging experiment, acquisition, processing, and analysis parameters have to be completely and accurately reported. This presentation will evaluate the current status of imaging reporting in the scientific literature and will walk you through the proper reporting parameters in some of the most commonly used UIC imaging systems.

Imaging Live Specimens: Challenges and Opportunities I, II, and III

Part 1: Imaging live samples, whether cells, tissues, or animals, requires careful consideration of contrast methods and imaging strategies to avoid distorting the sample's physiology. This presentation will provide some general concepts as well as UIC-specific applications. The emphasis will be on cellular imaging, but animal imaging will also be discussed. 

Part 2: Common methods to generate contrast and label specimens for live imaging will be discussed, with emphasis on fluorescent proteins and other genetically encoded indicators.

Part 3: Intravital and whole animal imaging, technologies, and applications.

Spectral Imaging and Linear Unmixing

Concept and applications of spectral imaging for separation of dyes with poorly resolved excitation and emission spectra.

A Beginner's Guide to FIJI Part I & II

This webinar is a beginner's introduction to FIJI software. FIJI is one of the most commonly used open-source image processing and analysis software. University Imaging Center Staff are skilled in FIJI and can guide clients new to the software as well as assist in making macros or plugins. This webinar will instruct beginners in navigating the graphic user interface, managing memory, installing plugins, opening files and image sequences, subtracting background, enhancing contrast, applying rudimentary filters, making color images, basic annotations, making montages, intensity projections, and movies. The slides will be saved on our webinar website so attendees can refer back to them or attendees can connect with UIC staff for individual help with FIJI.

Basic Segmentation with FIJI

If you are a newcomer to FIJI, we urge you to review the slides in A Beginner's Guide to FIJI, parts 1 and 2. In "Basic Segmentation with FIJI," we'll cover thresholding, working with binary images, distance transforms, watershed segmentation, plus regional and extended maxima and minima. This presentation covers some of the features in the MorphoLibJ plugin, which can be installed by going to Help > Update > Manage update sites > scrolling to IJPB-plugins and checking the box on the left > Close > Apply changes > quit and restart FIJI.

For those who wish to delve in deeply, there is a detailed manual for MorphoLibJ which can be downloaded here under the documentation section.

Recording Correction Note, please read!: During the presentation, the explanation for rolling background subtraction was unintentionally miscommunicated. Here is the correct explanation: The local intensity value for every pixel is determined by averaging over a very large ball around the center pixel. The ball's local averaged intensity is subtracted from the center pixel as the ball rolls over every pixel in the image. The radius of the rolling ball should be at least the size of the largest object that is not part of the background.

Optical Resolution I & II

Part 1: Review of current super-resolution techniques applicable to biological imaging.

Part 2: Survey of the latest advances with an emphasis on commercial applications.

FIJI in 3D: Three Dimensional Image Processing, Analysis, and Visualization

FIJI has a built-in 3D Viewer that we will introduce to you as well as the built-in 3D filters for image processing and the 3D Object Counter, which can quantify numerous metrics, such as volume, surface area, 3D intensity measures, locate centroids, bounding box dimensions, and more. Next, we will examine a plugin designed for 3D image analysis, the 3D ImageJ Suite of plugins, which also works well in FIJI.

Additional Online Learning Resources