Software installation
Setting up the acquisition PC
Before proceeding, ensure you are familiar with the hardware requirements. BakingTray is known to run on both Windows 7 and 10. Windows 10 LTSC is recommended for future-proofing.


This should ideally be set up using the built-in motherboard RAID, to keep the slots free.
Consult your motherboard manual and set the on-board SATA ports to RAID mode if necessary before installing Windows. Windows is stupid and fails to boot if you switch to RAID mode afterwards.
In the event that you do need to switch SATA mode and Windows complains (it will likely BSOD) then you can try the following
  1. 1.
    Just boot it into safe mode and it should automatically install the RAID drivers. After booting into safe mode once it should then be able to boot normally. If this fails, check whether the RAID drivers are installed (look on motherboard manufacturer' website and download the drivers) then try again.

Stopping random reboots

If using Windows 7 ensure you select the update setting that allows the user to choose when to install updates. For Windows 10 the story is more complicated.
You must do this because Windows 10 forces reboots and this can disrupt data acquisition.

Install software

After installing Windows and any hardware drivers you must install the following software:
  • MATLAB (tested on 2019a and 2019b, may not work on earlier versions). You should install the following toolboxes: Curve Fitting, Data Acquisition, Image Acquisition, Image Processing, Parallel Computing, Signal Processing, Statistics & Machine Learning. Some of those are not currently used by BakingTray but they may be in the future so it's easier to install them if possible. If you lack some of those toolboxes, just install as many as possible and file an issue if you run into problems.
  • PI software that came with your hardware: PI GCS, PI MATLAB GCS2, Stage database, USB driver, PIMikroMove, PITerminal, PIUpdateFinder
  • Putty
The following software is useful but not critical
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.

Installation and configuration of ScanImage

  • Install ScanImage. The old version (5.6.x) will work as will work but BakingTray is compatible with SI Basic too. SI Basic SI 2020.1.4 is well tested and support for SI 2021.0.0 will be in the master branch by the end of Sept 2021. Do not use earlier versions of Basic.
  • Follow the steps in Setting Up ScanImage
  • Now is a good time to check the noise on your amplifiers.

Installation of BakingTray

Clone the master branch of BakingTray and add to your path:
  • code
  • code/resources
  • code/components and its sub-directories
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:
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.