OMERO: Open Microscopy Environment

The Jackson Laboratory

Online

Feb 16 & 23, 2021

1:00 pm - 4:00 pm

Instructors: Erick Ratamero

Helpers: Dave Mellert, Eric Perlman, Neil Kindlon

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General Information

OMERO is an open source client/server system written in Java for visualizing, managing, and annotating microscope images and metadata. This workshop will cover viewing your data, annotating, working with regions of interest, analyzing OMERO data using ImageJ and create figures for publication. The specific contents will be tailored to the participants, so that they can use the knowledge to their own research problems.

Who: The course is intended for users at all levels of knowledge, including people who have never used OMERO.

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

When: Feb 16 & 23, 2021. Add to your Google Calendar.

Requirements: Participants must bring a laptop 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.

Post-workshop survey

Please complete this brief anonymous post-workshop survey to help us understand the impact of this training. Thanks!

Schedule

Day 1

01:00 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

Syllabus

Managing images

  • Accessing OMERO.web
  • OMERO.web interface and OMERO data structures
  • Annotations: tags, key-value pairs
  • Rendering settings
  • Searching, filtering, tag-searching

OMERO.iviewer

  • Viewing, rendering settings
  • Adding ROIs, measurements
  • Reading and Plotting Data

OMERO.figure

  • Adding images
  • Panels: resizing, aligning
  • Rendering settings
  • Labels and scale bars
  • Using results from Fiji
  • Zoom and pan
  • Paper settings
  • Exporting figures

OMERO data in Fiji

  • Basic plugin usage
  • Performing local analysis
  • Saving results to OMERO

Setup

To participate in a workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

Fiji and Omero

The base workshop content will require an installation of Fiji on the local machine, with the OMERO.insight-ij plugin. See these installation instructions.

VPN

Please connect to Global Protect VPN if you’ve never done so. Questions? Please contact the IT help desk at 207 288 1414.

Install the videoconferencing client

If you haven't used Webex before, ask the JAX IT Help Desk to download and install the Webex client for your computer.