Setting Up Overview

Before you start

You should first ensure you have the required hardware and that there is nothing obstructing you from acquiring data with ScanImage.

Setting up the PC

• Install a recent version of MATLAB. BakingTray has been tested recently on releases between R2017a and R2019b. We have noticed rare random hard-crashes of MATLAB in later releases (for sure in R2019a and R2019b). These were traced to 3D acceleration and occurred on both Win 7 and Win 10. Updating Nvidia drivers did not help but starting MATLAB in software OpenGL mode did get rid of the problem.
• 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.
• 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 or, better yet, do it with a setup.m file containing the line of this sort: addpath(genpath('C:\MATLAB\BakingTray\code')) This way you are robust to the possible changes of the directory structure in the future. The pathtool GUI will also work if you prefer.

Setting up the hardware

• Ensure the hardware is functioning correctly.
• The three-axis stage should be aligned with the imaging plane.
• The PID loops on the X and Y stages should be tweaked.

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 check the noise on your amplifiers.

Set up BakingTray

• 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.