OMERO walkthrough example

In this document, we go through a common workflow that a scientist wishing to use OMERO might follow:

  • Import data using the Desktop client.
  • View images using the OMERO.iviewer plugin.
  • Analyze images using a 3rd party tool, e.g. Fiji.
  • Generate a figure using OMERO.figure.

Description

In the first part, we first show how to import data by yourself and for yourself into OMERO using various import strategies. This will be mainly done using the OMERO.insight desktop client.

Second part of this import section will show how to import data for another user, using OMERO.insight. The user importing the data needs to have some admin or restricted-admin privileges. More information about restricted privileges can be found at https://docs.openmicroscopy.org/latest/omero/sysadmins/restricted-admins.html

The import for another user requires that the user doing the import has specific privileges. We will use the user importer1, this could be, for example, a facility manager.

We will show:

  • How to install the OMERO.insight desktop client on Windows, Mac and Linux.
  • How to import data for the user logged in using OMERO.insight.
  • How to select a target Project and Dataset or create a new ones in OMERO for the imports.
  • How to add Tags to imported images at the import stage, to facilitate the management of these images later in OMERO.server.
  • How to import data for other users in OMERO.insight.

View

View images in OMERO.iviewer

We introduce OMERO.iviewer, a 2D viewer which can open and browse multi-t, multi-z and multi-channel images and allows to draw and edit Regions of Interest. It also offers the ability to view several images at the same time and synchronize the view.

Description

We will show here:

  • How to open multidimensional images in OMERO.iviewer
  • How to change rendering settings in OMERO.iviewer and scroll through z and t
  • How to change the Lookup table and invert the displayed intensities for a particular channel
  • How to use the Histogram feature
  • How to zoom and rotate the image
  • How to create a maximum intensity Projection and save it
  • How to save a current viewport as png in OMERO.iviewer
  • How to use and synchronize multiple viewer windows inside OMERO.iviewer

Inspect intensities, draw and evaluate ROIs

Work with ROIs in OMERO.iviewer

In this section, we cover the ability of OMERO.iviewer to work with ROIs, to draw, edit, annotate and evaluate ROIs in the images is shown. In this way, a simple image analysis can be achieved, such as getting the intensity measurements inside the pixels of the ROIs and sizes of the ROIs, such as areas for polygons and lengths for lines and polylines.

Description

We will show:

  • How to inspect the intensities
  • How to draw ROIs on the image
  • How to view ROIs associated with different z or t planes
  • How to use the Planes tab in OMERO.iviewer to see the spread of ROIs in multi-z, t images
  • How to create comments on ROIs and enable and disable the ROI popups
  • How to produce simple analysis results from the ROIs and and export the results locally

Description

The following workflows should work both with ImageJ and Fiji, after these have been correctly set up with the OMERO plugin for Fiji/ImageJ.

Using the User Interface of the OMERO plugin, we will show:

  • How to connect to OMERO using the OMERO plugin for ImageJ/Fiji.
  • How to open an image from OMERO.server into Fiji/ImageJ.
  • How to manually save ROIs and measurements as CSV back to the original image in OMERO.server.
  • How to import a newly created image from Fiji/ImageJ into OMERO.

Present or publish data

Create figures using OMERO.figure