Starting BakingTray
Starting BakingTray for the first time
You should by now have run through the detailed hardware checks before proceeding with the instructions on this page.
Making default settings files
At the command line run BakingTray
. You will see something like this at the command prompt:
Editing the settings file
The component settings file describes the hardware BakingTray will use.
Navigate to the
SETTINGS
sub-directory and open thecomponentSettings.m
file in an editor. For now set the maximum and minimum stage positions to reasonably large values: we'll deal with them in detail later.
Editing the system settings file
The system settings file describes the system as a whole.
The default recipe
Also in the settings directory is a file called
default_recipe.yml
. The recipe files define the properties of an acquisition. When you start BakingTray,default_recipe.yml
is read. You may edit this file so BakingTray starts with different defaults. You may create multiple such files and manually load one after BakingTray starts. e.g. different recipes for different organ types.
Finalising hardware settings
Be careful with the following steps. Go slowly so as not to damage your hardware.
Place the vibratome and blade holder with blade in the correct position with respect to the objective. e.g. So the blade centered on the objective and the blade tip is about 30 mm from the axis of the objective.
Assemble the stages and place an empty water bath on top.
You can leave the objetive off for now in order to avoid damageing it.
Set the X/Y stages to 0 (their mid-points) and move the XYZ stage so that the middle of the sample is under where the objective would be.
Bolt the stage into place.
Raise the water bath until the waterbath lip is level with the widest part of the blade holder. Move the Y stage and determine the maximum and minimum positions you can go without the blade holder hitting the lip of the water bath.
Perform the same check for the X stage. Motions of the X stage could cause the bath to hit the vibratome or the objective. You may, therefore, want the objective in place when making this measurement.
Carefully raise the Z stage and determine the point at which the blade comes within about 0.5 mm of the sample platform. This is is the maximum Z position.
Edit the config file. Restart BakingTray. Ensure the positions are honoured. You might need to restart MATLAB for the new values to be honoured.
Altering blade tile (pitch) will require updating the max Z axis position.
Calibrations
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