Online
May 5, 12, 19, & 26, 2021
1 - 4pm
Instructors: Erick Ratamero
Helpers: Dave Mellert, Neil Kindlon, Nathan Rush
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Automated microscopy technologies have amplified the volume and complexity of image data such that biologists must rely on computer scientists for solutions and software. Fiji provides a huge variety of advanced image analysis solutions and a friendly user interface for researchers to develop innovative, cutting-edge pipelines for biological image analysis.
In this workshop, we will introduce basic concepts of image analysis and intermediate workflows using Fiji. By the end of this workshop, you will be able to automate the bulk your image analysis, making it faster, more consistent and reproducible. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Who: The course is aimed at graduate students and other researchers who want to use Fiji for image processing. Visitors from other institutions are welcome to participate. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
When: May 5, 12, 19, & 26, 2021. Add to your Google Calendar.
Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).
Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.
Contact: Please email susan.mcclatchy@jax.org or erick.ratamero@jax.org for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
Please be sure to complete this survey after the workshop.
| 13:00 | Image formation and introduction to ImageJ/Fiji |
| 14:30 | Afternoon break |
| 15:00 | Adjustments, measurements, stacks, colors |
| 15:55 | Wrap-up |
| 16:00 | END |
| 13:00 | Introduction to programming in Fiji macro language* |
| 14:30 | Afternoon break |
| 15:00 | Introduction to programming in Fiji macro language (Continued) |
| 15:55 | Wrap-up |
| 16:00 | END |
| 13:00 | Segmentation, Colocalization, Tracking |
| 14:30 | Afternoon break |
| 15:00 | Tracking, batch processing, introduction to scripting |
| 15:55 | Wrap-up |
| 16:00 | END |
| 13:00 | Fiji macro workshop – building your first macro, step by step |
| 14:30 | Afternoon break |
| 15:00 | Fiji macro workshop (Continued) |
| 15:45 | Wrap-up |
| 15:50 | Post-workshop Survey |
| 16:00 | END |
To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
We will use Webex for this course.
You will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (Fiji, etc..) and the window for the Webex video conference client open. In order to see both at once, we recommend using one of the following set up options:
Please download and install Fiji before the workshop.