Short Description

Well plate support for Icy, with an interactive well plate viewer and batch processing capabilities within Protocols



This plug-in reads image data from well plates acquired using supported High-Content Screening (HCS) systems, and presents them into an intuitive graphical user interface for easy browsing. It also allows batch processing on these well plates using the Protocols environment.

Here is a list of the HCS systems currently supported, and the folder that should be given to the plug-in for proper loading:

  • Opera (PerkinElmer): "Meas_..." folder
  • ScanR (Olympus): folder containing "experiment_descriptor.xml"

How to use

Interactive plate viewer

When starting the plug-in (hint: the search bar is your friend...), a file dioalog opens, asking you to select the folder containing the plate data (the file filters indicate the supported systems). See above for a list of supported systems and to know which folder to point to.

After selecting the plate folder, a progress bar indicates loading progress, and the well plate viewer appears.

Clicking on a well displays:

  • A sequence viewer with the first available field in the well. This viewer automatically updates to reflect any change in well or field selection based on user selection.
  • A close-up view of the selected well on the right-hand side panel, which additionnally displays the fields and their positions within the well (up to scale, yeah!!). These fields can be quickly browsed via the slider below the well, or directly by clicking on each field inside the well itself (warning: since display is up to scale, clicking on fields acquired with a 63x objective is slightly tricky, unless you have a ridiculously large screen!)

Batch processing using Protocols

Browisng is about as fun as it gets, but at some point you do need to get (some) results out. I'm happy to say that you can now transparently batch process entire well plates in the same way you would batch process image folders using Protocols.

To process well plates in batch, you just need to insert (or embed your existing protocol within) a block called "Well Plate batch" (searchable on the left-hand side panel). This uber-block contains a file selector which should point to the plate folder (the same as for the interactive viewer, see above), and as usual all you need is to create a link between the output of this folder and your inner protocol. Indicators will let you know what well/field is currently being processed, so you'll have the opportunity to guess how much time you have for a coffee (or nap).

As an extra bonus, a "well filter" field lets you process only a subset of wells according to the following syntax:

  • typing "A" will tell the protocol to only process all wells of row A
  • typing "A 03 B12" (notice the space between items) will tell the protocol to process wells in row A, column 3, and well B12 (note that wells are only processed once even if filters overlap, such as in this example with well A03)
  • typing just "3" (without the preceding 0) is technically valid, but may not be what you wish: it will process any well with a "3" in its name, i.e. A03, A13, A23, etc.

Contributions are welcome

The API is relatively straightforward, therefore if you feel like writing an adapter for your own system, you just need to publish a plugin in Icy that implements the WellPlateReader interface, and this plugin should automagically recognise and use it. 

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  • Version • Released on: 2018-07-18 11:09:31

    Added "Rectangle" Well shape support

  • Version • Released on: 2018-05-02 16:22:38

    fixed unused filter comination exception

  • Version • Released on: 2018-03-22 15:30:41

    Fixed lost fields on wells

  • Version • Released on: 2018-03-02 11:39:41

    Added thread yield signals

  • Version • Released on: 2018-02-27 14:52:02

    added source files

  • Version • Released on: 2018-02-27 14:06:04

    Parallelized Opera reader
    Position metadata added to each field

  • Version • Released on: 2017-09-26 18:00:58

    Opera: Added the plate folder in the sequence metadata

  • Version • Released on: 2017-07-11 13:13:26

    IX83: Fixed issue with "missing" fields in a well
    NEW: support for batch processing of well plates in Protocols

  • Version • Released on: 2017-07-10 02:31:14

    (ScanR) Fixed the pixel size

  • Version • Released on: 2017-07-10 02:20:18

    New: limited support for the Olympus ScanR system

  • Version • Released on: 2017-06-30 17:38:22