In response to the COVID-19 pandemic, the University Imaging Centers are continuing to provide status updates, and have implemented mandatory cleaning and safety protocols for all users using UIC resources. Please visit our sunrise safety protocols page to learn more 

Remote Support & Online Learning Resources

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Remote Analysis

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 uic-staff@umn.edu.

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.

Software Downloads

Fiji (Fiji is just Imagej)

Click here to download
  • A powerful free downloadable open source image processing package based on ImageJ.

Nikon NIS-Elements Viewer

Click here to download
  • 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

Click here to download
  • 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

Click here to download
  • Application for viewing, enhancing and processing Zeiss .czi files.
  • To install, register with Zeiss and download and install ZEN.

Imaris Viewer

Click here to download
  • A free 3D/4D microscopy image viewer for viewing raw images as well as those analysis within Imaris.

Leica Application Suite X (LAS X)

Click here to download
  • Application to open images acquired on the Leica SP5.

QuPath

Click here to download
  • QuPath is an open, powerful, flexible, extensible software platform for whole slide image analysis.

Olympus Fluoview Viewer

Click here to download
  • 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

Click here to download
  • Application for viewing and converting Huron TissueScope LE pyramidal tiff files.
  • Compatible with Window operating systems.

Apps

App Name: Resolution
Author: Andrew L. Barlow
Platforms: Android & Apple products
Description: Characterize your microscope objective lenses, see how well matched they are to your microscope's image acquisition system. Input the magnification, immersion medium (air, oil, glycerol or silicone oil), NA (numerical aperture) and wavelength of light (lambda), to calculate the lateral resolution, axial resolution and fluorescence brightness of the objective. Characterize your acquisition system (camera pixel size, camera binning and additional magnification) to check if you're sampling at Nyquist frequency. Each of your objectives can be saved and easily restored, and shared with other microscopists via e-mail, MMS, Linked-In or even Facebook (why not?). The equations used for the calculations can be displayed by selecting the "Show Equations" option from the App bar menu. The sources of equations are referenced in the "About" box.
 

 
App Name: Koehler Tutor
Author: Andrew L. Barlow
Platforms: Android & Apple products
Description: Learn how to set Koehler illumination on any microscope. Teach yourself, or teach others. The app simulates your microscope's controls and the images generated at the eyepieces, acting as a virtual microscope. The locations of the controls on your microscope stand are shown, and the correct way to use them is explained. Their effect on the image at the eyepieces is demonstrated.
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.

UIC Webinar Series

As part of our ongoing remote support to the University of Minnesota research community the University Imaging Centers has launched a live UIC webinar series featuring content tailored to our users' needs. 

As new webinar's are presented we will be updating this page to include the presentation slides.

We look forward to presenting this material and invite you to stay tuned for upcoming webinar announcements!

Digital Image Analysis

Overview:

  • 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)

Click here to view the webinar presentation PDF

Reproducibility in Scientific Research: Reporting of Imaging Experiments

Overview:

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.

Click here to view the webinar presentation PDF

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

Part 1

Overview:

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. 

Click here to view the webinar presentation PDF

 

Part 2

Overview:

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

Click here to view the webinar presentation PDF

 

Part 3

Overview:

Intravital and whole animal imaging, technologies and applications.

Click here to view the webinar presentation PDF

Spectral Imaging and Linear Unmixing

Overview:

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

Click here to view the webinar presentation PDF

A Beginner’s Guide to FIJI Part I & II

Part 1

Overview:

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.

Click here to view the webinar presentation PDF

 

Part 2

Overview:

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. 

Click here to view the webinar presentation PDF

Optical Super Resolution I & II

Part 1

Overview:

Review of current super resolution techniques applicable to biological imaging.

Click here to view the webinar presentation PDF

Part 2

Overview:

Survey of the latest advances with emphasis on commercial applications.

Click here to view the webinar presentation PDF

Tissue Clearing and Imaging Services at the University Imaging Centers

Overview:
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.

Click here to view the webinar presentation PDF

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.

Click here to view the webinar presentation PDF

Additional Online Learning Resources

NEUBIAS Academy

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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.

Learn more and register for upcoming webinars.