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Micro-Manager’s CRISP Control Plugin

Before You Begin

Make sure CRISP is part of your hardware configuration, if it isn't already there then add it with Micro-Manager Window > Tools > Hardware Configuration Wizard…. See if you need further guidance on how to set up your hardware configuration.

Accessing the Plugin

The Plugin comes default in current versions Micro-Manager; if you don't have it in Plugins > Beta, update Micro-Manager to the latest nightly build.

Fig. 1
Access the Plugin window
Micro-Manager Window > Plugins > Beta

Plugin Controls Explained

Fig. 2
CRISP Plugin's control window
The red rectangle indicates which axis the Plugin is controlling.


  • 1) IDLE: turns off the IR LED and stops position adjustments
  • 2) LOG CAL: puts the CRISP in Log Amp Calibration state and measures SNR
  • 3) DITHER: causes CRISP to dither in order to measure the Error #
  • 4) SET GAIN: puts the CRISP in Set Gain state
  • Reset Offsets: resets the focus offset to zero for the present position
  • Lock: sets the focal position
  • Unlock: unlocks the focal position
  • Save: saves the settings (for all of the spin boxes) onto the controller

Spin Boxes

  • LED Intensity: controls CRISP’s infrared (IR) LED from 0-100%
  • Gain: controls the gain multiplier or loop gain; decrease the value if CRISP seems to oscillate or jitter
  • Avg: the number of samples to be averaged
  • Obj NA: the objective’s numerical aperture

Check Box

  • Polling: directs the Plugin to poll or query the controller at frequent intervals for CRISP state, error number, and SNR; uncheck when done with the 4-step calibration

Reported Values

  • CRISP State: such as Idle, Calibrating, Ready, In Focus, etc.
  • Error #: during DITHER higher error values are better; after SET GAIN the Error # will be close to zero
  • SNR: (in decibels) should be at least 2 dB else CRISP performance may be unstable and lock will be lost easily; increasing LED intensity and performing the 4-step calibration again to increase the SNR
  • AGC: minimum of ~20 is acceptable for average samples; may be much higher for very reflective samples
  • Sum: indicates the amount of light hitting the photodiode; if outside 50-80, redo the 4-step calibration
  • Offset: the difference between the locked-in focal position and the current position

Quick Setup Guide

  • Start the 4-step calibration1) by clicking the 1) Idle button.
  • Enter the objective’s NA (which affects the dither).
  • Click the 2) LOG CAL button.
  • Check the SNR display. If <2 dB, click through the rest of the 4-step calibration, increase the LED Intensity, and begin the calibration again. If SNR is still low after the LED is at maximum intensity, proceed to the next step anyway.
  • Click the 3) DITHER Button.
  • Check the Error #. It must be at least +/- 100; if it isn’t, move the Lateral Adjustment Screw. The farther from zero the error number, the stronger the lock.
  • Press the 4) Set Gain button.
  • Press the Lock button to preserve the focal position. (Press the Unlock button to release CRISP's focus lock.)
  • If CRISP loses lock, repeat the calibration steps and try to get a higher error number after dithering.
Fig. 3
Lateral Adjustment Knob
Used to increase error number during dither

Additional Tips

If you would like CRISP to maintain focus at a certain position, but the error isn’t 0, use the Reset Offsets button to make your desired focal position have “0” error.

Further Reading Refer to CRISP : Continuous Autofocus System for a description of CRISP operation and troubleshooting guides.

Note that the 4-step calibration should always go through all 4 steps before re-starting; Log Amp Calibration has a countdown in the CRISP State display but otherwise you can quickly click through them to get back to the beginning.
Address: 29391 W Enid Rd. Eugene, OR 97402, USA | Phone: +1 (541) 461-8181
crisp_mm_plugin.txt · Last modified: 2019/12/12 23:14 by jon