Setting Up Overview

Before you start

• You will need a suitable PC and a functioning install of ScanImage 5. Testing has been done with the latest release of ScanImage 5.2 but BakingTray should also work with its premium equivalent and likely also with later versions.
• Linear scanners will work, but a resonant scanner is recommended for speed and because the system is better tested in resonant mode. Keep in mind that higher speed Cambridge resonant scanners have a smaller angular range and will produce images with more noticeable shot noise since the pixel dwell times are shorter. Nonetheless, a 12 kHz scanner works well with bright signals.
• You will need a 3-axis stage built from supported motion hardware. You may use different hardware, as it straightforward to write the control classes, but V-508 or V-551 stages from PI are strongly recommended.
• The stages 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. Also see Ragan et al for details on sample preparation.

Software installation

• Follow the installation notes for ScanImage.
• 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.

Configuring BakingTray

Edit the BakingTray settings files for your system. Pay particular attention to ensuring that the stages can not be moved out of bounds.

Configuring ScanImage

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. Next steps:

• De-noise and check the bias on your amplifiers since BakingTray disables the ScanImage offset correction.
• Adjust other settings in ScanImage