Z-stack acquisition in the Yokogawa CSU-W1 confocal microscope

Yokogawa CSU-W1 confocal laser microscope

The image acquisition software Andor iQ3 employed in the Yokogawa SU-W1 confocal microscope dose not seem very user-friendly to me. It took a while to figure out how to avoid the out-of-range error or starting the z-scanning in the midway.

Beginning at the beginning

To begin at the beginning, not at the middle, CHECK the Centre Z Scan when you right-click the RepeatZ in the protocol. I wasted a lot of time before figuring this out.


Procedure to take a z-stack

A brief memo.

  1. Select the protocol MCZ (in our case)
  2. Right click RepeatZ
  3. Click Centre Z Scan (IMPORTANT! otherwise, the scan will start at the center of the z-range)
  4. Select Edit in the same menu
  5. Focus down to the bottom of the zebrafish larval brain. (We are using an up-right microscope)
  6. Click Options, Setting, Next, set the range 1000 um to cover the entire brain
  7. Click Start to specify the starting plane, change the focus to the dorsal surface and click End to specify the last focal plane to be scanned.
  8. Next. (If you don’t get an out of range error, it went well. )