Short Description

Import data from the Opera high-content screening system straight into Icy


NOTE: this plug-in is in early stages of development and will improve over time. Feedback is highly welcome via the user forum

This plug-in allows Icy to import screening data sets acquired on the Opera system (ex-Evotec, now produced and sold by PerkinElmer). Eventually, this plug-in could be used to recognise other well-plate imaging systems.

In its current state, the plugin lets you select a folder containing the plate data and will:

  1. Detect the plate / experiment name, the plate number, and the channel colors (based on wavelength)
  2. Allow you to load either one or all wells at once
  3. Open a viewer containing the plate layout, where grayed wells contain image data
  4. When clicking on each well, all the images in this well (i.e. the positions) are loaded into a unique time sequence

Below is a (live) TODO list of the features implemented (or to come):

  • [DONE]  Recognize the wellplate name and shape (i.e. number of wells)
  • [DONE]  Read metadata: 2D resolution
  • [DONE]  Read metadata: fluorescence wavelengths
  • [DONE]  Read image data: FLEX 2D
  • [DONE]  Read image data: FLEX 3D
  • [DONE]  Display well-plate on screen
  • [TODO]  Read image data: TIFF (exported from FLEX by 3rd party software)
  • [TODO]  Display well positions on the upper-right-hand well diagram
  • [TODO]  Read image data: FLEX 2D + time
  • [TODO]  Read image data: FLEX 3D + time
  • [TODO]  Replace the plugin with an importer (enables drag’n’drop of the plate folder inside Icy)
  • [TODO]  Read metadata from other imaging systems

How to use this plugin

  1. Select the folder containing the plate image files (e.g. Meas_xx). Warning: do not select a folder containing multiple plates, this will not work.
  2. Click the “Run” button at the bottom of the interface to show the plate viewer
  3. Click on any grayed well to load the images contained inside the well (NB: multiple fields will be loaded as a single, timelapse sequence)


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  • Version • Released on: 2016-09-13 17:51:51

    Added helper functions to read a well plate in a generic way

  • Version • Released on: 2016-07-29 16:10:11

    * Fixed ordering of fields inside wells
    * Fixed wavelength extraction on 4+ channel data

  • Version • Released on: 2016-06-14 17:11:35

    Stop button to halt loading of large data sets

  • Version • Released on: 2016-06-14 17:00:57

    Re-uploaded jar file

  • Version • Released on: 2016-06-14 17:00:28

    Added a stop button to halt loading on big data sets

  • Version • Released on: 2016-05-25 11:55:48

    * Fixed display of 96 well plates
    * Well plate viewer now appears after loading the first image (and loads the rest in the background)
    * Each well plate has its own viewer

  • Version • Released on: 2016-05-24 19:24:28

    * New: support for TIFF data (exported from the IM software)
    * 24, 96 and 384 well plates are now displayed with the same final size (wells look bigger on small plates, smaller on large plates)

  • Version • Released on: 2016-05-24 14:24:32

    Added support for 3D data

  • Version • Released on: 2016-05-24 10:31:48

    * Well plate viewer now available!
    * FLEX data and metadata is now read directly from the raw file (bypassing Bio-Formats) => better handling of multi-channel data, and 3x faster file loading!!
    * WARNING: Z stacks not supported (will be in the next upgrade)

  • Version • Released on: 2016-05-17 14:31:43

    Yet another fix (Bio-Formats seems to have *serious* issues with Opera data)

  • Version • Released on: 2016-05-17 14:21:39

    Fixed a number of issues regarding metadata loading

  • Version • Released on: 2016-04-25 11:04:41

    Fixed an issue causing files read from a server wouldn't be loaded in the proper order

  • Version • Released on: 2016-04-20 18:44:46

    Fixed an issue while loading multiple series (images per well)

  • Version • Released on: 2016-04-20 17:42:09

    The data set now appears in Icy while the well plate is still being loaded

  • Version • Released on: 2016-04-20 16:53:36