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Introduction

In OMERO you are able to download most images in their original format. You can also export images as OME-TIFF, JPEG, PNG or TIFF images

The following table details the levels at which the different export formats are enabled. The * indicates usage of the Batch Image Export script (see below). The download of original data can be enabled or disabled for Images or Plates by sysadmin configuration. The table below shows the expected behaviour with the default configuration.

Export of images as OME-TIFF, JPEG, PNG or TIFF is not supported for large tiled images, typically above 3000 x 3000 pixels.


Operation Projects Datasets Multiple Images Single Images Plates Single Images in Plates Multiple Images in Plates
Download in original format X X X X X
Export as OME-TIFF X ✓ * ✓ * X ✓ *
Export as JPEG, PNG or TIFF X ✓ * X


Note

If an image was imported before OMERO version 5.0 it can only be downloaded in the original format if it was archived at import.



Using the Download menu

  1. Click on the Export icon in the toolbar.

    OMERO.insight


    ../images/exportDropdownInsight.jpg

    OMERO.web


    ../images/exportDropdownWeb.jpg


  2. Select Download from the drop-down to download the image in its original format.

    In OMERO.insight, choose the destination folder in the Download window and click Download.

    In OMERO.web the file will be downloaded according to your browser convention.


    ../images/exportDownloadInsight.jpg



  3. Select Export as OME-TIFF from the drop-down menu to export the image in OME-TIFF format.


    ../images/exportOMETIFFExport.jpg

    OMERO.insight

    Use the file finder in the Export window to choose the destination.

    Select the OME-TIFF version to export, from the drop-down in the bottom left.

    Click Export to create and download the OME-TIFF as a ZIP archive.


    ../images/exportOMETIFFInsight.jpg

    OMERO.web

    Click Create to generate the OME-TIFF using the latest version.

    The OME-TIFF is attached to the image as a ZIP archive.

    Click Download in the Activities window to download the archive.


    ../images/exportOMETIFFWeb.jpg


  4. Select the appropriate format to export the image as a JPEG, PNG or TIFF.

    In OMERO.insight, use File Finder in the Download window to select the destination.

    In OMERO.web the file will be downloaded according to your browser convention.

    OMERO.insight


    ../images/exportFormatsInsight.jpg

    OMERO.web


    ../images/exportFormatsWeb.jpg


  5. Note

    When an image or dataset is downloaded as a JPEG, PNG or TIFF, individual images for each channel and a combined-channel image are generated for the selected Z section or time point for the image(s). All generated images are contained in a ZIP archive.



Using the Batch Image Export script


  1. An alternative way to export multiple selected images or an entire dataset is to use the Batch Image Export script.

    This script enables a wide range of parameters to be configured before batch exporting.

    OMERO.insight


    ../images/exportBatchInsight.jpg

    OMERO.web


    ../images/exportBatchWeb.jpg


All Tutorial Material is available on line at: help.openmicroscopy.org

The Main OME website is at: www.openmicroscopy.org