Setting Up Overview

Before you start

• Ensure that you have the required hardware and that it's assembled and functioning.
• Ensure that you are able to acquire images with ScanImage. Testing has been done with the latest release of ScanImage 5.5 but BakingTray should also work with its premium equivalent and likely also with later versions.
• The three-axis stage should be aligned with the imaging plane.
• If you wish to cut the sample after each tile-scan you will need to bolt a vibrotome next to the objective. The procedure for doing this with a Leica unit is described by Economo et al.

Installing Drivers

• Install MATLAB. BakingTray was tested on 2016a through 2018a and should work on later releases.
• If using PI stages, install the PI drivers for the stages and follow the instructions for setting up the MATLAB PI interface. If you need to install the SDK in order to compile the PI drivers, you may find this link useful. The PI MATLAB code will need to be in your path. It should be located at C:\Users\Public\PI\PI_MATLAB_Driver_GCS2 once installed.

Software installation

This proceeds in two steps: 1) Installation and set up of ScanImage. 2) Installation and set up of BakingTray.

Installation and configuration of ScanImage

• Install ScanImage.
• Follow the instructions in "Setting up ScanImage" to correctly configure the scan settings.
• It is important that you accurately calibrate the number of microns per pixel in ScanImage. BakingTray uses this number to figure out where to move the stages. Also note the optional fine-tuning procedure.
• You should now De-noise and check the bias on your amplifiers since BakingTray disables the ScanImage offset correction.

Install and set up BakingTray

• Clone BakingTray and add to you path code, code/resources, code/components, and the sub-directories in code/components. You can use the function at BakingTray/addBTtopath.m to do this.
• Follow the instructions in "Starting BakingTray for the First Time".
• You will also want to familiarise yourself with the information on the settings files. Pay particular attention to ensuring that the stages can not be moved out of bounds.