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 leter 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.objectiveZSettlingDelay - The number of seconds to wait after each fast z motion before imaging the next frame. This number if fed directly into ScanImage. A value of 0.05 means 50 ms, which should be ample. If you blurring in the first few lines of each frame, increase this value.
• SYSTEM.enableFlyBackBlanking - ScanImage has the ability to blank the laser turn-arounds. This is mainly used to avoid photo-damage in vivo when using resonant scanners (and to a lesser extent linear scanners). We don't care much about bleaching and photo-damage, since our tissue is dead and we image each frame only once. On the other hand, the blanking can lead to ringing in the amplifier for samples with high autofluoresence. Set this parameter to false to switch off blanking or true to enable it. See what works better for you.
• 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.