Parameter Explanations

Image Source

ALICA offers 3 different options of acquiring images from MicroManager:

  • MM Core Images are drawn directly from the circular buffer. This method is the fastest, and recommended in most cases, since it can smoothly function whenever the camera is acquiring images.
  • Live mode Images are drawn from the Datastore associated with the current live mode view. Use this if you wish to do some on-the-fly processing using the MicroManager pipeline, before passing the image to Analyzer.
  • Next acquisition Images will be drawn from the Datastore associated with the first acquisition that is started afterwards.

ROI

Using the live view, you can select a region of interest to constrain the analyzed area (for example if the density of fluorophores is uneven, or the analysis of full image takes too long).

Controller tick rate

This value in milliseconds defines how often the Controller queries the Analyzer, and adjusts the laser output.

Laser

  • Max Power Maximal power setpoint of the laser. ALICA will not adjust the laser power above this value.
  • Deadzone [%] The minimum adjustment to the power setpoint that the controller may make as a percentage of the current value. Adjustments to the laser by an amount less than this are not permitted, which prevents unnecessary fine-tuning of the laser.
  • Virtual If checked, the output is not passed to the device. Useful for debugging or preview of parameters.