News, Events, Workshops, & Webinars

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.

• Presentation PDF
• Presentation Recording

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.

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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.

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• Presentation Recording

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)

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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. 

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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.

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

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Spectral Imaging and Linear Unmixing

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

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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 included under the documentation section on Github.

• 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.

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