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.
Workshops
While we are constantly evolving and expanding our curriculum, past workshops have included: Core Microscopy Concepts, Sample Preparation, Microscopy Instrumentation & Software, Quantitative Analysis, and 3D Reconstruction.
Registration is open for the UIC hosted Imaris 9.9 Workshop!
Taylor Smith (Oxford Instruments) will be offering a remote workshop on the new features and capabilities of the recently released Imaris 9.9 update.
This workshop will center on the new capabilities of the software and will not be a training session starting from zero. Some Imaris experience is necessary to take full advantage of this opportunity.
Click Here to Register!
Tentative schedule:
Wednesday, July 13, 9 a.m.-1 p.m. New features of Imaris 9.9, specifically pixel classification segmentation and filament tracer
Friday, July 15, 9 a.m.-1 p.m. Four 50 min blocks are devoted to specific, real-world samples.
- EM, SBF-SEM dataset, or TEM.
- A non-neuronal, filament tracer example (subcellular filaments, vessels)
- Large cleared brain sample
- TBD
Questions? Please email us at uic-staff@umn.edu!
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 |
Webinars
Past Webinar Presentations
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
Presentation PDF
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.
Presentation PDF
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)
Presentation PDF
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.
Presentation PDF
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.
Presentation PDF
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.
Presentation PDF
Part 3: Intravital and whole animal imaging, technologies, and applications.
Presentation PDF
Spectral Imaging and Linear Unmixing
Concept and applications of spectral imaging for separation of dyes with poorly resolved excitation and emission spectra.
Presentation PDF
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.
Part 1: Presentation PDF
Part 2: Presentation PDF
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.
Presentation PDF
Presentation Recording
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.
Presentation PDF
Part 2: Survey of the latest advances with an emphasis on commercial applications.
Presentation PDF
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.
Presentation PDF
Additional Online Learning Resources
- How to Optimize Imaging with Nikon Elements Software, Part 1
- How to Optimize Imaging with Nikon Elements Software, Part 2
- How to Optimize Imaging with Nikon Elements Software, Part 3
- MyScope Microscopy Training
- MicroscopyU
- iBiology Microscopy Series
- Micron Advanced Microscopy Course
- ZEISS ZOYC Webinars and online learning content
- ZEISS On-demand training and tutorials
- Introduction to Fiji/ImageJ for bioimage/microscopy analysis.
- Dave Mason's online workshop using Fiji for image analysis.