Verifying hardware operation

Once you have the hardware assembled and connected to the PC it is time to check that it functions correctly.

Installing BakingTray

Before proceeding, clone the master branch of BakingTray and add its code directory and all sub-directories to the MATLAB path. It is best to do this with a setup.m file containing the line of this sort: addpath(genpath('C:\MATLAB\BakingTray\code')) This way you are robust to the possible changes of the directory structure in the future. The pathtool GUI will also work if you prefer.

Vibratome

Most vibratomes consist of a DC motor that turns a cam which produces lateral motion of an assembly that in turns holds the blade. You will now ensure you can set the vibratome to run at a desired speed and also stop the vibratome.

The Z-jack

The X/Y/Z sample translation stage is pushed up and down by what we will refer to as a Z-Jack. You will now ensure that you can connect to the motor controller and issue motion commands. Some motor controllers (such as that on the TC1000) are not calibrated and so you will also need to measure how many motor pulses there are per mm. For this you will need a Mitoyo measuring gauge sold by ThorLabs and an arm of some sort to clamp it to. You can clamp to the thicker portion with a 9.5 mm diameter right below the main body (see the ThorLabs CAD PDF from the link above).

Basic connection

First clear the stage and ensure that it can hit nothing.

• Connect
• Issue small motion commands

Ensuring limit switches work and repeatability is good

Calibrating

If necessary you will need to calibrate the Z-stage

X/Y Stages

The X/Y sample stages translate the sample during a tile scan and drive the sample into the blade during cutting.

PIFOC

The PIFOC will be controlled by ScanImage but now is a good time to get to know it and ensure it's behaving well. Mount the objective you will be using into the PIFOC and start ScanImage.