Fundamentals of bioimage analysis with ImageJ
This two-day workshop will first introduce participants to the basics of image processing and general bioimage analysis workflows with ImageJ. On the second day, participants will expand their ImageJ skills to create automated workflows with macro programming; and apply their knowledge to solve specific image analysis tasks.
You also have the option of joining our Open Office session on Tuesday afternoon (limited spots available!), where we will give you advice on your project!
Requirements: Participants are expected to bring a laptop, further instructions will be sent about one week before the workshop. No prior programming knowledge required!
Catering: Sandwiches and coffee breaks will be catered for all days.
Registration Fees: 800 kr.
Program
This program is subject to change.
Day 1 — Introduction to Bioimage Analysis with ImageJ
| Morning - Session 1 | Introduction to ImageJ and digital images |
| Morning - Session 2 | Thresholding and noise removal |
| Afternoon - Session 1 | Binary masks and morphological operations |
| Afternoon - Session 2 | Signal quantification & Colocalization |
Day 2 — Automation and Machine Learning
| Morning | ImageJ Macro Programming |
| Afternoon | Extending ImageJ with Plugins |
| Closing | Open Office |
Location
Bioimaging Core Facility Aarhus, Department of Biomedicine, Skou Building 1116
10 Høegh-Guldbergs Gade
Aarhus, 8000
Denmark
About the Organisers
Bioimaging Core Facility at Biomedicine
(Aarhus University)
The Bioimaging Core Facility was founded in 2019 with the aim to make high-end imaging and image analysis equipment available to everybody for affordable fees.
The Imaging Core Facility currently services more than 200 active users per year.
DBI-Infra IACF
The Danish Bioimaging Infrastructure (DBI-Infra) Image Analysis Core Facility (IACF) provides open services in image analysis to life scientists and medical researchers. We offer both in-person and remote support, helping you to visualize, analyze, and extract quantitative information out of your bioimaging datasets from anywhere.
Our team of experts is here to discuss your image analysis needs, guide and train you in the most suitable software solutions, or develop a complete image analysis workflow tailored to your scientific project. We leverage an extensive hardware and software infrastructure designed for remote image analysis, including a pool of latest-generation workstations, innovative High Performance Computing and data exchange services, and a broad range of bioimage analysis software tools.
The facility actively promotes open science and the most efficient data sharing with the scientific community according to the FAIR principles. We are collaborating with the Danish e-Infrastructure Collaboration (DeiC), the Network of European BioImage Analysts (NEUBIAS) and Euro-BioImaging, and we are engaged in multiple training and dissemination activities.