BakingTray
  • BakingTray Documentation
  • Getting Started
    • Hardware requirements
    • Known issues
    • Initial Installation
      • Software installation
      • Setting up ScanImage
    • Hardware setup
      • Motor Setup
        • PI stage setup
        • Calibrating a linear actuator
        • Verifying stage motions
      • Setting up a VT1000 vibratome
      • Setting up the laser
    • Finishing the install
      • Check the noise on your amplifiers
      • Starting BakingTray
      • Settings Files
      • Calibration
        • Basic calibrating procedures
        • Calibrating image size
        • Achieving high stitching accuracy
        • Fine-tuning positioning accuracy
        • Stitching tweak walkthrough
    • Stitching data
  • Users
    • Introduction
    • Sample preparation
    • User Guide
      • Starting BakingTray
      • Step 0: Loading the sample
      • Step 1: Setting imaging parameters
      • Step 2: Preparing the sample
      • Step 3: Selecting the imaging area
      • Step 4: Starting the acquisition
      • Step 5: Concluding the acquisition
      • Setting up checklist
      • Resuming an acquisition
      • Manual ROI acquisitions
    • Excitation choices
    • Choosing imaging settings
    • Troubleshooting
      • Hardware problems
      • Computer problems
      • Cutting problems
      • Imaging problems
    • Data structure
    • autoROI
  • Developers
    • Developers
      • Code overview
      • Developer notes
      • Motion control classes
      • The recipe file
      • Auto-ROI
      • Simulated mode
      • Contributing
    • FAQ
    • Gallery
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On this page
  • Setting up a Faulhaber motor controller with a Leica VT1000
  • Connecting the controller
  • Connect to the controller
  • Set the drive parameters
  • Confirming the vibratome can communicate with BakingTray
  • Running without the encoder
  1. Getting Started
  2. Hardware setup

Setting up a VT1000 vibratome

PreviousVerifying stage motionsNextSetting up the laser

Last updated 3 days ago

Setting up a Faulhaber motor controller with a Leica VT1000

The Leica VT1000 vibratome head works well and requires just a DC motor controller. The motor and encoder in a VT1000 is made by Faulhaber so if you buy a Faulhaber motor controller it is easy to run the unit at a defined RPM. The motor is a Faulhaber 3540K012C () connected to a HEDS-5500 encoder (). The following instructions are written assuming you are using a Faulhaber MCDC 3006 S RS controller. These are no longer made, instead you will want to buy an MC5005 S RS. The physical connections on the device are different, since they are not screw terminal, but otherwise everything should be fairly self explanatory with the new controller.

It is a good idea to connect the encoder, since you have it and you will get better control of motor speed this way.

There are instructions further down below for what to do if you did not (or can not) hook up the encoder.

Connecting the controller

Hook up the motor to a 12V DC 1 A supply.

Snip off the green connector coming off the motor on the vibratome, strip the leads, and tin the bare wires.

Hook up to the controller as shown below. Note the far right motor +/- leads power the motor; here these wires looker thicker for those cables as the originals were extended. The thinner black and red wires are power for the encoder. The encoder sensor wires are the remaining two: white and brown.

Finish off the install by hooking up the serial cable to the PC (with the MC5005 S RS you can use a USB cable). Power on the device!

Connect to the controller

Click "Establish Connection" in the top left. Select the COM port of your device then "Next". The select the first entry in the drop-down ("Motion Control V2.x") and select "Next", then "Next" through the next window.

You will then see a window that lists your controller:

Click "Finished" and the main window will now look like this:

Set the drive parameters

Press "Select motor" under the "Establish connection" button. You will need to make a motor with the right properties. Press "Create" in the following window:

Now fill in the next window as follows:

Now "Save". Confirm the settings on the original page look as follows. The encoder is a HEDS-5500-A which has a spec sheet that says it has 500 lines/rev. So set the pulses per rev to 500 pulses/rev. Correct that if needed and hit "Next"

Skip the next window describing the gear train ("Load transmission"). Just "Next" through it.

In the following window ("Factor of inertia"), J_Load should be "20".

In the next window, just press 'Next' to select the default "quiet running".

"Finished" on the summary page. This sends the parameters to the motor and you should say "Yes" when offered to store these to the device.

You can test the device by going to the "Operate motor" section and running the motor at 3200 RPM, which is the default speed in BakingTray.

The motor should run almost silently with the blade holder and blade attached, assuming everything is bolted down tightly. Quit the software.

Confirming the vibratome can communicate with BakingTray

You should have already added BakingTray to your path. The following sample session shows how to start up the class for controlling the vibratome and sending commands to it.

>> f=FaulhaberMCDC('COM2'); % connect to the vibratome on COM port 2

If you have run through all of the steps, ensure that the controller is in the correct mode for running with the encoder:

>> f.set2CONTMOD;

You do not need to run that again: the mode of the encoder has been stored to its non-volatile memory.

You can now control the motor in RPM:

>> f.startVibrate(1000);  % 1000 RPM
>> f.startVibrate(2000);  % 2000 RPM
>> f.stopVibrate; % Stops the motor
>> delete(f) % disconnects from the controller

Running without the encoder

If you could not set the motor up with the encoder using the above steps then follow this section. Perform the following steps with the vibratome securely mounted, blade in blade holder, and blade holder mounted. Nothing should be loose. Do not excessively tighten things, though, this is not needed.

Without the encoder it is easy to run the vibratome motor far harder than the manufacturer intended. Start at slow speeds and be sure you know how to cut power to the device if you need to.

The following sample session shows how to start up the class for controlling the vibratome and sending commands to it.

>> f=FaulhaberMCDC('COM2'); % connect to the vibratome on COM port 2
Setting up Faulhaber MCDC3006 DC motor controller.
Motor max speed: 60 revs per second.

You now need to tell the controller to run without the encoder:

>> f.set2IXRMOD;

You do not need to run that again: the mode of the encoder has been stored to its non-volatile memory.


%Let's start a gentle vibration
>> f.startVibrate(5); % You should now see a modest vibration of the blade
>> f.stopVibrate;  % And we stop it

You should consider the sample speed setting, which is the input argument to startVibrate, to be in arbitrary units. The goal now is to identify a reasonable speed setting for slicing the sample.

% Try a range of speeds and stop once it becomes more noisy
>> f.startVibrate(10); % quiet
>> f.startVibrate(11); % quiet
>> f.startVibrate(12); % still quiet
>> f.startVibrate(13); % Getting loud: vibrations are clearly audible
>> f.startVibrate(10); % <--- Back off a few steps. Make a note of this setting.
>> f.stopVibrate;

% Terminate the session
>> delete(f)
Closing connection to Faulhaber MCDC motor controller

If you run the vibratome too fast you will wear our the axle or the bearings and may need to replace the whole unit after a year or two. Make a note of the vibrate speed chosen above. You will later use this when making the BakingTray settings file and only modify if it if you notice cutting problems.

The following instructions are for , which you should install now. Note it is possible your version of Motion Manager 6 won't look exactly like what is shown below, but it should be close enough.

Press "Next" and in the next window you will enter the properties of the motor. You might find that your window looks different to the following. In which case use the to find the correct values. Remember that in this datasheet 1,7 means 1.7.

Note that BakingTray can also run devices such as the Leica VT1200 (the unit used by ) by gating its operation with a TTL pulse via the class.

Faulhaber Motion Manager 6
3540K012C datasheet
Economo et al
JaneliaLeicaContoller
datasheet
datasheet
Faulhaber_establish_connection
snip_strip_tim
Faulhaber_Motor_connections
Faulhaber_establish_connection
Faulhaber_Connection_to_device
Faulhaber_Connected_full_window
Faulhaber_motor_selection
Faulhaber_motor_selection__edit_motor
Faulhaber_Motor_selection_properties
Faulhaber_motor_selection
Faulhaber_Motor_Selection_Factor_of_inertia