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Importing Data into OMERO

This section covers the general procedures for importing data into OMERO at the Leiden Cell Observatory. OMERO allows to organize our imaging data in a structured way. This makes the data findable and accessible for your research group.
To make this possible, the data needs to be uploaded in a structured way and need to include the correct metadata. If you are not sure how to approach this, please contact the OMERO admins or the data steward at your institute for help.

Overview

OMERO.insight is the primary tool for importing data. This client is:

Basic Import Workflow

  1. Prepare Your Data

    • To make data accessible to others, use a consistent naming convention of your Project and Dataset names.

    • It is advised to organize your data according to the ISA model, which is a standard for organizing and sharing scientific data. This model organizes data in a hierarchical structure, which is similar to the way we organize our data in OMERO. The ISA model consists of three main components:

      • Investigation: An overarching description of the research project, this can be a consortium with multiple collaborators
      • Study: A specific research question within the investigation
      • Assay: A specific assay or analysis within the study

    ISA model

    The ISA data model (adapted from Sansone et al. (2012))

    • Try to match the structure of your data in OMERO with the organization of your experiments in your Electronic Lab Journal (RSpace).
    • Prepare any metadata you want to include at the time of import.

  2. Launch OMERO.insight

    • Connect to the server: omero.services.universiteitleiden.nl
    • Login with ULCN credentials
    • Navigate to your Group/project space

  3. Import Process

    • Use File > Import or the import icon
    • Select the files for import
    • Choose or create projects/datasets or Screens/Plates
    • Use the omero.mde plugin to add metadata
    • Add any additional tags or annotations
    • Review and start import

Data Organization

Project Structure

OMERO uses a two-level organization system: - Projects (top level)
- Datasets (within projects)

Organize Datasets within Projects; avoid storing Datasets outside Projects

✅ Recommended Structure:
Project 1 (ISA: Study)
├── Dataset 1 (ISA: Assay 1)
│   └── image 1, etc.
└── Dataset 2 ((ISA: Assay 2)
    └── image 1, etc.

❌
├Dataset 1 (ISA: Assay 1)
│└── image 1, etc.
└Dataset 2 (ISA: Assay 1)
 └── image 1, etc.
To include the ISA:Investigation in the OMERO structure you should annotate the Project with metadata. This can be done with the omero.mde plugin.

For (High-content) imaging screens OMERO offers: - Screens (top level)
- Plates (within screens)

Planning Your Import

Before starting a large import:

  1. Plan your project/dataset structure
  2. Prepare experimental metadata at time of import
  3. Consider file type specific requirements

Next Steps