The Settings Files

BakingTray uses configuration files located in the SETTINGS directory.

System Settings

The so-called "system settings" are those that describe parameters of the rig that are unlikely to change between sessions. This includes things like how fast the stages are supposed to move, the settling time of the PIFOC, and general features of the cutting cycle. BakingTray.settings.readSystemSettings parses systemSettings.yml and creates it if does not already exist. You will be prompted to edit the file. The settings of course can be changed at a later time. Here is what each parameter means:

• SYSTEM.ID - A string defining the unique name of your microscope. This will allow you to distinguish between different microscopes should you have multiple systems.
• SYSTEM.xySpeed - The target maximum speed of your X/Y stage in mm/s. With the fast PI stages a value of 100 mm/s or even a little more is not unreasonable.
• SYSTEM.cutterSide - set to 1 if the vibrotome is on the right as you look at the system. Set to -1 if the vibrotome is on the left.
• SLICER.approachSpeed - The speed in mm/s with which the sample is brought to the cutting start point. You can leave this at around 25 mm/s. It's not critical.
• SLICER.vibrateRate - Vibrate rate of the blade in cycles per second. This will vary by vibrotome. If you are using a vibrotome where this setting is applied in hardware, you can set this to anything you like.
• SLICER.postCutDelay - Number of seconds to wait for the cut slice to settle to the bottom of the bath. About 5 seconds is reasonable.
• SLICER.postCutVibrate - The vibrate rate to use during the post-cut delay period. We find that hugely reducing the blade speed (e.g. to 3 Hz) allows the slice to slide off the blade.

Component Settings

The componentSettings.m file defines how the hardware components of the rig are to be set up. It is read by BakingTray.settings.readComponentSettings and created if it does not exist. Instructions for filling in this file are present in the comments of that file. It's vital this file is filled in correctly to avoid damage to your system, particularly for the motion components. For instance, the motion limits of the stages are defined in this file and are used to make it impossible for out of bounds motions to be executed.

You should first run your stages using the manufacturer's software to familiarise yourself with them. When filling in the component settings file, keep the following in mind:

• The X stage moves left/right as you look at the rig and positive is to the right. Middle of the travel range is 0.
• The Y stage moves front/back as you look at the rig and positive is away from you. Middle of the travel range is 0.
• The Z stage pushes up the sample and positive is up. Fully lowered is 0.
• All motion commands need to be in mm.

For instance, you may find that your X stage moves from "0" to "100" mm with zero on the left. This means the middle of the motion range is 50 mm, not 0 mm, and positive values are to the left not to the right. Thus, the motion commands going to this device will need to be modified. The easiest way of doing this is to create a stage class specific to this stage and use the transformInputDistance and transformOutputDistance properties to effect the conversion. These properties can also be used to change units. Examples:

• The haydon43K4U class which converts between stepper motor steps and mm.

Startup File

If present, a file named SETTINGS\startup_bt.m will run automatically once BakingTray has started. This is done by BakingTray.m You may put whatever code you want to execute into this file. It is not sanity checked!