Short Description
Import data from the Opera high-content screening system straight into Icy
Documentation
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:
- Detect the plate / experiment name, the plate number, and the channel colors (based on wavelength)
- Allow you to load either one or all wells at once
- Open a viewer containing the plate layout, where grayed wells contain image data
- 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
- 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.
- Click the “Run” button at the bottom of the interface to show the plate viewer
- Click on any grayed well to load the images contained inside the well (NB: multiple fields will be loaded as a single, timelapse sequence)
