Resuming an acquisition
It is possible to resume an acquisition that stopped for whatever reason. The following steps can be performed even if MATLAB crashed or the acquisition was interrupted by a power cut.
Perform the following steps to resume an acquisition:
- Select Sample > Resume Acquisition from the BakingTray menu. Load the recipe file from the acquisition directory containing the sample you wish to resume.
- You will be asked to confirm whether you wish to resume the acquisition.
- Press "Yes" and double-check the parameters in the recipe and prepare GUI.
- You will then be presented with a new GUI asking how the acquisition should be resumed. e.g. if the last section was partially completed, should the existing data be discarded and the section re-imaged.
- You are responsible for turning the PMTs back on. Similarly for ensuring the laser is on and the shutter is open.
- The Acquisition GUI will now appear. Press "Bake" to start the acquisition. You only need to do another preview scan in exceptional circumstances (see below).
- It is not necessary to do another preview scan and repeat the auto-thresh under most circumstances. If you are re-starting the acquisition because of an issue related with the auto-ROI, or because somehow how the sample vanished, etc, then of course you should do another preview and another Auto-Thresh before pressing Bake.
- If you have reason to think the sample surface might have moved (e.g. you have changed the blade) then you might want to take a preview scan first and repeat the auto-thresh. Then watch how it cuts and tweak objective height.