The University Imaging Centers offers remote support to researchers by consultation on experiment design, imaging strategies, visualization, processing and analysis. UIC Staff are available by phone, email, and videoconference to discuss your research imaging and analysis questions.
If you have an analysis need or question please contact us at email@example.com.
Free Analysis Software
Depending on your analysis or visualization needs, several vendors provide free viewing or “light” software packages. If you need more complex analytical features, we encourage you to download Fiji (Fiji Is Just ImageJ), a powerful free downloadable open source image processing package based on ImageJ.
Fiji (Fiji is just Imagej)
- A powerful free downloadable open source image processing package based on ImageJ.
Nikon NIS-Elements Viewer
- NIS Elements Viewer for PC and Mac is a free, "light" proprietary software for viewing images collected on several of our Nikon microscopes.
- Application for viewing and converting (.tif) Nikon .nd2 files.
- Full NIS Elements software is available. If you require the full software please fill out the form above or contact UIC staff.
Zeiss 90-Day Version of ZEN (blue edition) of ZEN core
- You can now get the full processing and analyzing power of ZEN imaging software for your PC or laptop at home, for free, for a full 90 days.
Zeiss ZEN Lite for TIRF and Spinning Disk Confocal
- Application for viewing, enhancing and processing Zeiss .czi files.
- To install, register with Zeiss and download and install ZEN.
- A free 3D/4D microscopy image viewer for viewing raw images as well as those analysis within Imaris.
- QuPath is an open, powerful, flexible, extensible software platform for whole slide image analysis.
Olympus Fluoview Viewer
- This software will read the data captured by a FV1000/FV500/FV300. Images saved with the FV file format (OIF, OIB, FV Multi-Tiff) can be read.
- This software is intended for image reading. Image capture, measurement, analysis, 3D function, etc. can not be performed using this software.
- For Windows operating systems.
HuronViewer for TissueScope LE
- Application for viewing and converting Huron TissueScope LE pyramidal tiff files.
- Compatible with Window operating systems.
Remembering all of the steps required to set Koehler illumination can be tricky, and this app will serve as a useful reminder whenever you wish to check that the configuration of your instrument is correct.
Setting Koehler illumination generates an evenly illuminated field of view, reduces stray light, and allows you to set the balance between resolution and contrast.
As part of our ongoing support to the University of Minnesota research community the University Imaging Centers has launched UIC webinars featuring content tailored to our users' needs.
Join us for the next presentation!
Title: Introduction to Rebus Esper, an integrated spatial omics platform with advanced optics, automated fluidics, and flexible assay chemistry
Presenters: Tarif Awad, PhD, VP Scientific Affairs, Rebus Biosystems
- Time: 12:30 - 1:30 PM
Traditional cell biology and microscopy recently fused with genomics to create a powerful new paradigm for studying biology: spatial omics. A range of methods and approaches are emerging, most of which focus on one class of biomolecules and often compromise sensitivity, specificity or dynamic range in favor of higher plex. Rebus Biosystems has developed the Rebus Esper™, an integrated platform that combines resolution-enhancing Synthetic Aperture Optics (SAO) with automated fluidics, to enable multiple types of assays for detecting biomarkers in tissue sections at single-molecule, subcellular resolution. The streamlined workflow minimizes hands-on time and reduces variability by automating the laborious steps required for multiplexed single-molecule detection. Multiple assay chemistries will be available for the Rebus Esper platform. The Esper High Fidelity Assay for spatial transcriptomics automates single-molecule FISH chemistry to quantify 30 custom genes across ~1 cm^2 of tissue in ~2.5 days. New assays in development will combine protein staining with RNA expression, as well as allow the use of FFPE tissue, a challenging but important sample type for clinical and translational research. Bioinformatics and a data analysis pipeline are integral to the Rebus Esper system, supporting novel analysis and visualization tools to uncover the power and beauty of spatial omics results. As with assay chemistries, analysis tools will continue to evolve as new, more complex types of spatial omics data emerge.
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
- 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
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.
Common methods to generate contrast and label specimens for live imaging will be discussed, with emphasis on fluorescent proteins and other genetically encoded indicators.
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 softwares. 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.
In this webinar we will cover several more beginning FIJI features such as calibrating images, orthogonal views, 3D rotations, and working with hyperstacks. Then we will venture into beginning quantitation of 2D images. We will threshold and make binary images, segment the binary image with a watershed segmentation, explore the region of interest (ROI) manager, and finally perform arithmetic and logical operations with the image calculator. You will also have a few tips about data result tables in FIJI.
Optical Super Resolution I & II
FIJI in 3D: Three Dimensional Image Processing, Analysis, and Visualization
Overview: Join us as we venture into three dimensional bio-image quantitative analysis!
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
To learn more about underlying principles of image analysis, we recommend watching this iBiology course on Bioimage Analysis (45 min).
NEUBIAS Academy is a new initiative, aimed to provide sustainable material and activities focused on Training in Bioimage Analysis.
Live Online Courses will provide interactivity with the audience (e.g. exercises in virtual breakout rooms), live Webinars will target larger audience with specific topics, software tools, theoretical content or critical updates, from introductions to concepts to very advanced implementations.