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Importing ImageXpress HCS.ai Data to OMERO

Data from the ImageXpress HT.ai is saved in the .JDCE file format. This is a relatively new file format and is not directly supported for upload to OMERO using OMERO.insight, as OMERO.insight by default uses an older version of bioformats.

  • For now you can only upload data to OMERO from the ImageXpress microscope PC and the ImageXpress analysis PC, where we adjusted OMERO.insight.
  • To upload the data in OMERO.insight, browse to the folder with the data. Select only the JDCE file. Be aware that if you have acquired z-stacks there is a folder with the z-stack data and a folder with the maximum intensity projections. Generally it is recommended to upload the z-stack data, but you can additionally also upload the maximum intensity files if needed.
  • When you have acquired tile scans with the ImageXpress it is possible that the images are too large to be shown directly in OMERO. In that case follow the procedure below and convert the images to OME-TIFF first.

Warning After converting images to OME-TIFF for OMERO, you will not be able to open them with InCarta software (that is the image analysis software provided by the vendor of the ImageXpress). Always keep the original files if you may need to analyze data with InCarta in the future.

Converting Files to OME-TIFF

When you need to convert your files to OME-TIFF this can be done using the NGFF-converter, which preserves most metadata from the original files.

Step-by-step Instructions

  1. Locate your .JDCE file

    • Go to the folder containing your ImageXpress data.
    • Each experiment may have several folders, such as experiment, experiment_z_stack, and experiment_montage, each with its own .JDCE file.
    • If you acquired z-stacks, experiment_z_stack contains the original z-stack, experiment contains maximum intensity projections, and experiment_montage contains stitched images.

  2. Open NGFF-Converter

    • Launch the NGFF-Converter application. This application is installed on the image analysis workstation next to the ImageXpress.
    • Drag your .JDCE file into the application window. You will see a popup. NGFF-converter

  3. Select Output Format

    • Choose OME-TIFF as the output format and press OK.

  4. (Optional) Split Large Datasets

    • By default, data is saved as a single OME-TIFF file. For large datasets, this file can become very large and hard to handle.
    • To split the OME-TIFF file per field-of-view:
    • Press the Settings button next to your file in the main window.
    • Use the right arrow on top of the popup to select TIFF
    • Click Advanced Settings.
    • Toggle Split Series on.
    • Click Apply.

  5. Run the Conversion

    • Press Run and wait for the conversion to finish. By default the converted files will be saved in the same folder.

Upload to OMERO

  1. Upload with OMERO.insight
    • Open OMERO.insight.
    • Look for the *.companion.ome file generated by the converter. Select this file to upload. You do not need to select all the other OME-TIFF files.
    • In OMERO.insight, create a new screen with your desired name and upload the data. OMERO.insight