OMERO: Open Microscopy Environment

The Jackson Laboratory

Online

Nov 9 & 14, 2022

1-4pm EST

Instructors: Erick Ratamero

Helpers: helper one, helper two

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General Information

OMERO is a modern client-server software platform for visualizing, managing, and annotating scientific image data. OMERO lets you import and archive your images, annotate and tag them, record your experimental protocols, and export images in a number of formats. It also allows you to collaborate with colleagues anywhere in the world by creating user groups with different permission levels. This workshop will teach you to view and annotate data, work with regions of interest, analyze OMERO data with ImageJ, and create figures. The specific contents will be tailored to the participants, so that they can use the knowledge to their own research problems.

Who: This workshop is only open to Jackson Laboratory employees. The course is intended for users at all levels of knowledge, including people who have never used OMERO. No programming experience is needed.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Nov 9 & 14, 2022. 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.

Surveys

Please be sure to complete this survey after the workshop.

Post-workshop Survey

Schedule

Day 1

1:00	Basic image management
2:15	Break
2:35	Viewing, analyzing and publishing images using OMERO plugins
4:00	END

Day 2

1:00	Using OMERO from external software
2:30	Break
2:50	Publishing with OMERO.figure
3:50	Post-workshop Survey
4:00	END

Setup

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.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, 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 (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

Fiji and OMERO

The workshop will require an installation of Fiji on the local machine with the OMERO plugin. Please contact the IT help desk for assistance with installation.

Fiji: https://fiji.sc/

OMERO.imagej plugin: See these installation instructions.

VPN

Please connect to Global Protect VPN if you plan to be off campus during the training.