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This addon contains a workflow engine, which allows you to execute workflows on a set of plates or experiments.

A workflow is a set of actions that are performed in a fixed order (or 'flow'). Several examples of how workflows can be used:

  • Perform cell classification using a threshold on cytoplasm marker intensity.
  • Calculate 'polished' features by applying a median polish algorithm on a plate.
  • Detect key features by performing principal component analysis on a large set of features.
  • Perform a custom data or curve fitting method using R packages.


To install the Workflow addon, select Help > Install New Software. In the site list, select Phaedra Updates. Check the Workflow item in the addon list, and click Next.

Running a Workflow

This topic explains how to run workflows. If you wish to design a new workflow, please contact a Phaedra administrator.

To run a workflow on a plate or experiment, right-click on it and select Workflows > Open workflow.


In the dialog that appears, you can select one of the available workflows.


When you select a workflow and click Open, the workflow view will open.

To run the workflow, click on the green Run All button in the toolbar (or press Shift + F7).


While the workflow is running, the traffic lights of the workflow actions will change from red (queued)to green (completed). When all actions have been completed, a message will appear.

At that point, you can close the workflow view. If Phaedra asks you to save the workflow, select No.