> For the complete documentation index, see [llms.txt](https://bakingtray.mouse.vision/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://bakingtray.mouse.vision/getting-started/known-issues.md).

# 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](https://github.com/SWC-Advanced-Microscopy/BakingTray/issues). The more notable issues are as follows:

* During acquisition with linear scanners [Issue #20](https://github.com/SWC-Advanced-Microscopy/BakingTray/issues/20) or a high level of averaging with resonant scanners [Issue #234](https://github.com/SWC-Advanced-Microscopy/BakingTray/issues/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](http://www.ni.com/en-gb/support/model.usb-6343.html) 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](https://github.com/SainsburyWellcomeCentre/BakingTray/issues/13). 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.

* 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.