> 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/users/user_guide.md).

# User Guide

- [Starting BakingTray](https://bakingtray.mouse.vision/users/user_guide/step_01_starting-bakingtray.md)
- [Step 0: Loading the sample](https://bakingtray.mouse.vision/users/user_guide/step_00_sample_into_microscope.md)
- [Step 1: Setting imaging parameters](https://bakingtray.mouse.vision/users/user_guide/step_02_setting-up-imaging-parameters.md)
- [Step 2: Preparing the sample](https://bakingtray.mouse.vision/users/user_guide/step_03_preparing-the-sample.md)
- [Step 3: Selecting the imaging area](https://bakingtray.mouse.vision/users/user_guide/step_04_selecting-the-imaging-area.md)
- [Step 4: Starting the acquisition](https://bakingtray.mouse.vision/users/user_guide/step_05_starting-the-acquisition.md)
- [Step 5: Concluding the acquisition](https://bakingtray.mouse.vision/users/user_guide/step_06_concluding-or-restarting-the-acquisition.md)
- [Setting up checklist](https://bakingtray.mouse.vision/users/user_guide/checklist.md)
- [Resuming an acquisition](https://bakingtray.mouse.vision/users/user_guide/acq_resume.md)
- [Manual ROI acquisitions](https://bakingtray.mouse.vision/users/user_guide/manual_roi_acquisitions.md)