BIOP Operetta Tools

Scripts and tools used for the PerkinElmer Operetta System at the EPFL BioImaging & Optics Platform. For a more thorough tutorial on our recommendations for using our PerkinElmer Operetta and data export protocols, you can check out our BIOP Wiki page

Export flatfield images

The Harmony software from the Operetta system is capable of providing "flatfield corrected" images of acquisitions on the fly. Exporting these flatfield images is however not trivial.

Upon discussion with PerkinElmer, we have been allowed to share the following script that allows the export of images with the flatfield correction applied to the images.

Warning This script requires a valid Harmony license to work, as it calls PerkinElmer's software directly.

Flatfield export script and protocol

Before running the script

Make sure that the Export_Flatfielded_Images_biop.bat contains the location of the Acapella.exe file. For us it is currently in %programfiles%\PerkinElmer\Harmony 4.9\ACServ\ but this will change with newer versions of Harmony.

Make sure you download both Export_Flatfielded_Images_biop.bat and Export_Flatfielded_Images_biop.script to a local folder before starting the export protocol.

Export prototol

1. Export the measurements from Harmony with “Referenced Images”, i.e. you will just get an “index.ref.xml” file.

2. Run the batch (.bat) file located in this repo's Operetta flatfield export folder.

3. The script will then ask for an index.xml file. Select the file that was created during the Harmony export of the previous step.

4. The script will create a new folder and write all flatfield corrected images into that folder.

5. It will also generate a new appropriate index.xml file.

The resulting flatfield iamgesd can now be processed either using the BIOP Operetta Importer or imported onto OMERO with all metadata intact.

Note The orignal script provided by PerkinElmer is provided in the Original Script folder. It uses a different naming convention for the resulting XML file, (appends _flex to the name), which is incompatible with importing the data to OMERO.

Working with Operetta data

To load, view or resave Operetta data, whether it is flatfieled or not, the following tools are available:

| Tool | Link | Pros | Cons | | -----|------|------|------| | BIOP Operetta Importer | https://github.com/BIOP/ijp-operetta-importer | Can load, downsample, fuse and export tiled versions as tiffs(*) | Requires yet another resave export. | | BDV Playground | https://imagej.net/plugins/bdv/playground/bdv-playground | Has a dedicated Open [Operetta Dataset] command for BigDataViewer. Many export modes. Convenient to visualize data per well | Visualization and export are in beta. | | QuPath | https://qupath.github.io/ | Native support to open the index.xml file| Only displays individual fields (no stitching). Can become unresponsive with too many images in the QuPath project|

(*) The BIOP_Operetta_Import.groovy script in the deprecated folder is the precursor to the BIOP Operetta Importer plugin which is available though the PTBIOP Update site