News, Events, Workshops, & Webinars

Workshops & Webinars

Overview

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.

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Past Workshops, Webinars, & Events

Title Event Type Attendees Date(s)
Bell Museum's SciPride 2025 Demonstration

325

June 14, 2025
FIJI for Beginners: Basic Image Processing with FIJI Webinar

64

May 1, 2025
MERSCOPE: Mapping the Future with Spatial Genomics Lunch & Learn

25

April 1, 2025
Top 10 tips for ensuring scientific integrity for your publication images Webinar

40

December 19, 2024
ZEISS Lattice Lightsheet 7: Long-term volumetric imaging of live cells Seminar

53

November 19, 2024
UIC & MSI Image Analysis Half-day Workshop Workshop

25

November 14, 2024
Beginning concepts in image processing with FIJI Webinar

65

October 24, 2024
TriTom - a multimodal platform for in vivo 3D imaging of small animals Webinar

29

October 17, 2024
MSI X501 - Image Analysis Workshop: Analyzing Fluorescence Microscopy Images in FIJI Workshop

25

August 12, 2024
Eclipse JI: Ai-Driven microscopy for the future of imaging Webinar

29

February 29, 2024
Confocal Workshop (SH) Workshop 9 July 6-8, 2022
UIC Multiplexed Ion Beam Imaging (MIBI) Workshop Workshop 43 June 29-30, 2022
Segmentation Workflows with FIJI Workshop 11 March 25, 2022
Segmentation Workflows with FIJI Workshop 13 March 23, 2022
Confocal Workshop (JH) Workshop 10  November 2-4, 2021
Confocal Workshop (JH) Workshop 15 October 12-14, 2021 
Midwest Association of Core Directors (MWACD) (TCF Bank Stadium) Conference 150 October 16-18, 2019
UIC Nikon SoRa Workshop (CCRB) Workshop 30 October 16, 2019
Confocal Workshop (JH) Workshop 11  July 16-18, 2019
Confocal Workshop (JH) Workshop 12  Jun 18-20, 2019
Live Animal Image Acquisition and Analysis Workshop (JH) Workshop 4 April 10, 2019
Confocal Workshop (JH) Workshop 10 July 11-13, 2017
Confocal Workshop (JH) Workshop 10 June 6-8, 2017
Live Cell Workshop (CCRB) Workshop 8 March 8-9, 2017
Confocal Workshop (SH) Workshop 5 December 13-15, 2016
UIC & UMII Image Analysis Workshop (CCRB) Workshop 15 December 1, 2016
Confocal Workshop (CCRB) Workshop 9 November 1-3, 2016
Confocal Workshop (JH) Workshop 24 May 17-19, 2016
UIC & UMII Workshop: An Introduction to Image Analysis (CCRB)  Workshop 21 October 23, 2015
UIC & UMII Workshop: A Hands-On Introduction to FIJI (SH) Workshop 13 August 5, 2015
UIC & UMII Workshop: A Hands-On Introduction to FIJI (SH) Workshop 18 July 29, 2015
UIC & UMII Workshop: A Hands-On Introduction to FIJI (SH) Workshop 15 July 22, 2015

Webinar Presentation Archive

FIJI for Beginners: Basic Image Processing with FIJI

In this webinar, UIC staff member and Lead Image Data Analyst Mary Brown will introduce beginning concepts in image analysis as well as use of FIJI software. Topics that will be covered include denoising, background subtraction, the signal histogram, the line intensity profile plot, filtering/feature enhancement, and contrast enhancement. This webinar is targeted to researchers with little to no experience with FIJI or image analysis.


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.


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)

 


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 included under the documentation section on Github.

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.


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.

News & Events

UIC Newsletter

A periodic publication highlighting the latest news and updates from the University Imaging Centers

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Issue Archive

Issue Archive

A periodic publication highlighting the latest news and updates from the University Imaging Centers

Archive Link Issue Date
March 2025 3/31/2025
September 2024 9/23/24
August 2024 8/5/2024
May 2024 5/1/2024
April 2024 4/15/2024
March 2024 3/18/2024
February 2024 2/19/2024
February 2024 2/5/2024
December 2023 12/18/2023
December 2023 12/11/2023