# 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) --- # Agent Instructions This documentation is published with GitBook. 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