Known Issues

In general BakingTray is very stable and almost all acquisitions complete without errors. The full list of issue can be found on the BakingTray issue tracker. The more notable issues are as follows:

• During acquisition with linear scanners Issue #20 or a high level of averaging with resonant scanners Issue #234 there are multiple instances of duplicate tiles appearing in the preview window. This does not affect the saved data.

• We use an NI USB-6343 to control the PMT gains. This works but we see the following bug: there is a rare chance that, when BakingTray is open, switching off the PMTs causes MATLAB to crash. We work around this by disabling PMT auto-on and having BakingTray issue the PMT off command at the conclusion of acquisition only. We experience no problems or acquisition failures when working like this.

Hardware-related issues.

• PI stages that have relative encoders and need referencing sometimes need to be referenced in PI's MikroManager before they will work in BakingTray.

• PROBLEM: Coherent lasers rarely switch off or close the shutter during the first section. This has never happened later in the acquisition. SOLUTION: Deleting the files in the acquisition directory and re-starting the acquisition.

• PROBLEM: Systems gets hung up during cutting. The V551 stages pick up the cutter through the bath and the controller thinks they have not stabilised. SOLUTION: Mount the cutter more solidly so it can't transmit vibration as easily. Check vibratome is not being driven too hard. Change the settings on the stages so they are more tolerant to small errors.