Software installation

Setting up the acquisition PC and installing required software and drivers.

Before proceeding, ensure you are familiar with the hardware requirements.


BakingTray requires Windows and will not run on Linux or Mac OS. Installs have been known to run on Windows 7, 10, and 11. If possible install Windows LTSC as it is less aggressive with updates and has less useless crap installed by default.

Disabling Random Windows Reboots

You must ensure that Windows will not attempt to install updates or reboot the system without permission.

If using Windows 7 ensure you select the update setting that allows the user to choose when to install updates. For Windows 10 and 11 the story is more complicated. It is still recommended you install updates when the system is idle: BakingTray will not be affected if you do this.

Ensure Windows Does Not Enter Sleep Mode

Configure the Windows Power settings such that the PC will never go to sleep when unattended.

Data storage and RAID

You will want at least 4 TB of local storage, on a physical volume separate from the OS drive. If you have a resonant scanner this must be either an SSD or a platter disk striped RAID with at least two drives (2 disk RAID 0 or 4 disk RAID 0+1). A single 8 TB SSD works very well.

Raid Mode

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. 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.

Software versions

BakingTray has not been extensively tested on a range of MATLAB and ScanImage versions. Only general indications are provided here. It is the intention that BakingTray can be run on recent MATLAB and ScanImage versions, so you should feel free to use the latest versions of both and file an Issue if something fails. However, it is known that certain combinations do not work. MATLAB R2019b to R2021b are known to work with ScanImage SI Free v5.6-1 up to Basic 2023.0.0. MATLAB versions R2022b and R2023b seem not to be compatible with ScanImage (at least up Basic 2023.0.0).

Install Software

After installing Windows and any hardware drivers you must install the following software:

  • MATLAB. 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.

  • NI DAQmx v 19.0 or newer if you do not have a vDAQ.

  • PI software that came with your hardware: PI GCS, PI MATLAB GCS2, Stage database, USB driver, PIMikroMove, PITerminal, PIUpdateFinder

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

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 possible future changes in the directory structure. The pathtool GUI will also work if you prefer, but do not add the base BakingTray directory and all its sub-directories: this may have unintended consequences.

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