# BakingTray

## BakingTray

- [BakingTray Documentation](https://bakingtray.mouse.vision/readme.md): Serial-section extension for ScanImage
- [Hardware requirements](https://bakingtray.mouse.vision/getting-started/hardware_requirements.md): This page describes the hardware you ought to have to run BakingTray using ScanImage.
- [Known issues](https://bakingtray.mouse.vision/getting-started/known-issues.md)
- [Initial Installation](https://bakingtray.mouse.vision/getting-started/initial-installation.md)
- [Software installation](https://bakingtray.mouse.vision/getting-started/initial-installation/installing_software.md): Setting up the acquisition PC and installing required software and drivers.
- [Setting up ScanImage](https://bakingtray.mouse.vision/getting-started/initial-installation/setting-up-scanimage.md): Basic set up of ScanImage for use with BakingTray
- [Hardware setup](https://bakingtray.mouse.vision/getting-started/hardware-setup.md)
- [Motor Setup](https://bakingtray.mouse.vision/getting-started/hardware-setup/motor-setup.md)
- [PI stage setup](https://bakingtray.mouse.vision/getting-started/hardware-setup/motor-setup/pi-stage-setup.md)
- [Calibrating a linear actuator](https://bakingtray.mouse.vision/getting-started/hardware-setup/motor-setup/calibrating_actuator_mm.md): Calibrating a linear actuator
- [Verifying stage motions](https://bakingtray.mouse.vision/getting-started/hardware-setup/motor-setup/verifying-stage-motions.md)
- [Setting up a VT1000 vibratome](https://bakingtray.mouse.vision/getting-started/hardware-setup/setting_up_vt1000.md)
- [Setting up the laser](https://bakingtray.mouse.vision/getting-started/hardware-setup/laser_setup.md)
- [Finishing the install](https://bakingtray.mouse.vision/getting-started/finishing-the-install.md)
- [Check the noise on your amplifiers](https://bakingtray.mouse.vision/getting-started/finishing-the-install/exploring-amplifier-noise-and-bias-in-scanimage.md)
- [Starting BakingTray](https://bakingtray.mouse.vision/getting-started/finishing-the-install/starting-bakingtray-for-the-first-time.md): Starting BakingTray for the first time
- [Settings Files](https://bakingtray.mouse.vision/getting-started/finishing-the-install/the-settings-files.md)
- [Calibration](https://bakingtray.mouse.vision/getting-started/finishing-the-install/calibration.md)
- [Basic calibrating procedures](https://bakingtray.mouse.vision/getting-started/finishing-the-install/calibration/basic-calibrating-procedures.md)
- [Calibrating image size](https://bakingtray.mouse.vision/getting-started/finishing-the-install/calibration/calibrating-the-number-of-microns-per-pixel-with-scanimage.md)
- [Achieving high stitching accuracy](https://bakingtray.mouse.vision/getting-started/finishing-the-install/calibration/achieving-high-stitching-accuracy.md)
- [Fine-tuning positioning accuracy](https://bakingtray.mouse.vision/getting-started/finishing-the-install/calibration/fine-tuning-positioning-accuracy.md)
- [Stitching tweak walkthrough](https://bakingtray.mouse.vision/getting-started/finishing-the-install/calibration/example_stitching_correction_walkthrough.md): Tweaking BakingTray and StitchIt for high stitching accuracy
- [Stitching data](https://bakingtray.mouse.vision/getting-started/stitching-data.md)
- [Introduction](https://bakingtray.mouse.vision/users/introduction.md)
- [Sample preparation](https://bakingtray.mouse.vision/users/sample_prep.md)
- [User Guide](https://bakingtray.mouse.vision/users/user_guide.md)
- [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)
- [Excitation choices](https://bakingtray.mouse.vision/users/choosing-wavelength.md)
- [Choosing imaging settings](https://bakingtray.mouse.vision/users/choosing-imaging-settings.md)
- [Troubleshooting](https://bakingtray.mouse.vision/users/troubleshooting.md)
- [Hardware problems](https://bakingtray.mouse.vision/users/troubleshooting/hardware-problems.md)
- [Computer problems](https://bakingtray.mouse.vision/users/troubleshooting/computer-problems.md)
- [Cutting problems](https://bakingtray.mouse.vision/users/troubleshooting/cutting-problems.md)
- [Imaging problems](https://bakingtray.mouse.vision/users/troubleshooting/acquisition-problems-and-solutions.md)
- [Data structure](https://bakingtray.mouse.vision/users/data-structure.md)
- [autoROI](https://bakingtray.mouse.vision/users/autoroi_setting_up.md)
- [Developers](https://bakingtray.mouse.vision/developers/developers.md)
- [Code overview](https://bakingtray.mouse.vision/developers/developers/code-organization.md)
- [Developer notes](https://bakingtray.mouse.vision/developers/developers/developer-notes.md)
- [Motion control classes](https://bakingtray.mouse.vision/developers/developers/motion-control-classes.md)
- [The recipe file](https://bakingtray.mouse.vision/developers/developers/the-recipe-file.md)
- [Auto-ROI](https://bakingtray.mouse.vision/developers/developers/autoroi_dev.md): Details for developers and power-users
- [Simulated mode](https://bakingtray.mouse.vision/developers/developers/simulated-mode.md)
- [Contributing](https://bakingtray.mouse.vision/developers/developers/contributing-to-bakingtray.md)
- [FAQ](https://bakingtray.mouse.vision/developers/faq.md)
- [Gallery](https://bakingtray.mouse.vision/developers/gallery.md)