PerkinElmer/Revvity Operetta Importer Command and API

Features

This repo has a clear(ish) API and a nice SciJava InteractiveCommand

Documentation

We are hosting the JavaDoc as GitHub pages at https://biop.github.io/ijp-operetta-importer/

The main class you should focus your attention on is OperettaManager

If you'd like to see some examples on how it can be used, please check the Scripts folder. This contains a few Groovy examples on how to call the Operetta Importer API

Installation in Fiji

Go to Help > Update...

Click Manage Update Sites

Activate the PTBIOP update site.

Usage

Standard Operetta Import

Go under Plugins -> BIOP -> Operetta importer -> Operetta importer or type Operetta importer in the search bar.

Select input folder

• Select the folder to analyse. It should contain all individual images, WITH the index.idx.xml file.
• Click on Ok

Select data to analyze

1. Click on Choose Wells button to select a subset of available wells.
2. Click on Choose Fields button to select a subset of available fields.
3. Click on Preview Well slice button to get a preview of the data
4. Write down a subset of channels to analyze
5. Write down a subset of slices to analyze
6. Write down a subset of frames to analyze

Select processing options

7. Choose a downsample factor. BE CAREFUL: DO NOT SELECT 0. If you don't want to do any downsampling, select a downsampling of 1.
8. Check the box if you want to average pixels during downsampling.
9. Select a fusion option
   • Do not fuse fields
   • Fuse with stage coordinates => put fields next ot the other without doing any blending
   • Fuse using Grid/Collection stitching => correctly stitch fields with affine transforms

9a. For Grid/Collection stitching ONLY, you can choose some settings to fine tune the stitching (compute overlap, regression threshold, relative & absolute displacement threshold). The definition of the settings can be found in the plugin documentation page

10. Select a flipping option
    • Do not flip
    • Flip horizontal
    • Flip vertical
    • Flip both
11. Select a projection option
    • No Projection
    • mean
    • min
    • max
    • median
    • std
    • sum
12. Select the min/max values of the intensities

Output and Saving

13. Choose a directory where to save the output images
14. Check the box to save the fused images as OME-TIFF and to generate the corresponding companion.ome file. This option only works if you have fused fields together.

15. A message is written at the bottom of the UI to inform you on the size and time the analysis will take. Finally, you can click on Process.

---

Operetta Archive Import (Harmony 4.9+)

This plugin also supports importing data from Harmony Archive format, which stores images in a different structure with an SQLite database and UUID-named TIFF files.

Go under Plugins -> BIOP -> Operetta importer -> Operetta Archive Importer...

Expected Archive Structure

The Harmony Archive has the following folder structure:

Harmony-Archive/
├── XML/
│   └── MEASUREMENT/
│       └── <uuid>.xml          <- Select this file
└── IMAGES/
    └── <uuid>/
        ├── IMAGES.sqlite
        └── *.tiff files

Select the XML file

• Navigate to and select the XML file located at Harmony-Archive/XML/MEASUREMENT/<uuid>.xml
• The plugin will automatically derive the images folder from the XML file path

The plugin will:

1. Generate an OME-XML companion file (.companion.ome.lazy) from the archive metadata
2. Open the companion file with Bio-Formats
3. Launch the same interactive import dialog as the standard Operetta importer

Once the companion file is generated, subsequent imports will reuse it (skipping regeneration).

Processing Options

After the archive is loaded, you will see the same interactive dialog as the standard Operetta importer, with all the same options for:

• Well and field selection
• Channel, slice, and timepoint selection
• Downsampling and averaging
• Field fusion and stitching
• Z-projection
• OME-TIFF export