Over the past few years, I’ve often battled the Micromanager MDA window, when needing to perform high speed triggered acquisitions. While the system works well for multi channel Z stacks, running timelapse 2 channel streams, or “Z first” streams, didn’t work well. To overcome this, I’ve written a script that pulls all of the MDA user settings out of the window, loads up the Triggerscope, and captures the sequence.
This approach gives any user of the triggerscope far greater control over how sequences are run, and offers users the ability to customize external device commands if needed.
I’ve cooked up a brief video overview here, with some example screenshots of the results on an oscilloscope below.
- If you’d like to use or check the script out, it can be found on my GitHub site here.
- Please note this requires updated firmware (V 600 or up)
A basic example of a Z stack in a single channel is shown below. In this configuration, 1 channel is selected in the MDA window, and a single Z stack is collected. The Yellow line indicates intensity of a laser or LED on Ch1, the pink line indicates the Z voltage output, and the blue line indicates a TTL input from the camera.
In the next example, output from a “channel first” Z capture is shown. Here Channel is prioritized, so the system runs Ch1 , then captures all Z frames, thens witches to Ch2, and captures all Z frames.
Next, is an example of a capture previously impossible in MM. In this capture we stream 3 time loops back to back, with no delay.
Next up is an example of a “Z First” capture, where all channels are acquired for a single Z position.
Finally, a multi channel example can be seen in this image, with 2 channels running in a time series.
Those are the highlights – I hope others find this useful!
-Austin