General concepts

Here we introduce general concepts about OMERO: image import, metadata upload, management, annotation, search and server-side scripts.

This section shows how to import data using the Desktop client, the Command Line Interface (CLI) and OMERO.dropbox. It also covers advanced import features and post-import processing steps used mainly in the context of the Image Data Resource (IDR).

The section shows the possibilities of getting images from OMERO. These can be described as “export” (new image, usually a jpeg, tiff or png is created from the original image saved in OMERO) or “download” (the original image, in the original format is downloaded from OMERO).

This section covers the general concepts of OMERO. Those concepts are demonstrated using the Web client. This section introduces the data management functionalities of OMERO, shows how to annotate data and demonstrates how to search for data and metadata. Also, the management of groups and users is presented, both in the Web client as well as on the command line.

This section describes how to run, write and manage the OMERO server-side scripts. Server-side scripts can be written in different programming languages but you will need to invoke the scripts using a Python wrapper.