Analysis of microscopy data with Fiji
Fiji is powerful and free image processing software — a "batteries-included" distribution of ImageJ, bundling many plugins which facilitate scientific image analysis.
Registration
The workshop will take place in the Holman Reading Room in the Biomedical library, and is free to UPenn graduate students, postdocs, faculty, and staff.
Overview
Fiji is the ‘batteries included’ version of the venerable ImageJ software. It bundles together many popular and useful ImageJ plugins for image analysis into one installation, and automatically manages their dependencies and updating. Fiji is easy to use and install - in one-click, Fiji installs all of its plugins, features an automatic updater, and offers comprehensive documentation.
Getting set-up
To participate in the workshop, please plan to bring your laptop with charging cord, and download and install Fiji sofrware.
Agenda
The morning will focus on learning the essentials with Fiji, and the afternoon will delve into more advanced functionality via plugins.
| start | end | topic |
|---|---|---|
| 9:00 | 9:30 | Breakfast and setup |
| 9:30 | 11:00 | Image data and Fiji essentials |
| 11:00 | 11:15 | Short break |
| 11:15 | 12:15 | ROIs, Measurements, and Thresholding |
| 12:15 | 1:00 | Lunch break |
| 1:00 | 1:30 | The Analyze Particles plugin |
| 1:30 | 2:30 | Filters and background subtraction |
| 2:30 | 2:45 | short break |
| 2:45 | 3:45 | Colocalization |
| 3:45 | 4:30 | Quick tour of useful plugins |
About your instructors
Andrea Stout, PhD started the CDB Microscopy Microscopy Core at the University of Pennsylvania in 2006 and has been its director ever since. Over the years she has taught hundreds of researchers how to use light microscopes and how to work with image data. From 2017-2022 she directed and taught a course on quantitative image analysis (CAMB 7090) using Fiji.
Allison Jamieson-Lucy, PhD is a light microscopy specialist for the CDB Microscopy Core. Her PhD work was in cellular biology and as an undergraduate she studied biochemistry and visual arts. She brings cross-disciplinary expertise in visual communication along with knowledge of quantitative techniques to provide training and education in image acquisition, analysis, and presentation.
