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Downloading and Exporting Data

This page describes how to download and export data from OMERO.

Downloading a lot of data

If you would like to download a large amount of data from OMERO, e.g. for data sharing for a publication. Please reach out to the OMERO admins. We can help using a script to export the data more efficiently.

OMERO.web Downloads

Export Formats

With OMERO you can export in different formats Standard Formats - Original Format: Exact copy of the uploaded file - OME-TIFF: Standard microscopy format with OME metadata - JPEG/PNG: Only for presentations/publications - TIFF: Original pixel data, can be used for image analysis

Quick Downloads

Access downloads through the OMERO web interface:

  1. Locate your data
  2. Click the download button at the right panel
  3. Choose export format: - Download... Original files - Download Original Metadata Download original metadata only - OME-TIFF format - JPEG format - PNG format - TIFF format

Download from OMERO web

Web Browser Timeout Limitation

Connections via the web browser automatically disconnect after 1 minute (60s), so often you won't be able to download large files. For larger datasets, use OMERO.insight instead.

OMERO.insight Downloads

Large Dataset Downloads

  1. Launch and log into OMERO.insight
  2. Navigate to your dataset
  3. Click the download button
    Download in insight
  4. Select export format

Downloads proceed in the background - no progress bar is shown, but the process remains active.

Fiji Downloads

Alternatively you can use the OMERO Fiji plugin for downloading data. You can find more information here