Background: 
We assume here you have finished Lab 8. In this more quantitative look at blaberus spines you will use a precise Thor linear actuator (DRV001) to probe a individual spines for their response to angular deflection (and rate of deflection, and direction). Two linked LabVIEW programs, running simultaneously, will be used to control the probe and collect spike response data. All data will be saved to MATLAB data files (.mat) and then analyzed in MATLAB itself, rather than in a MATLAB script running in LabVIEW.

Blaberus and the probe will be set up and viewed with an AO dissecting microscope. The microscope is additionally compatible with a microscope camera which can be used to capture a video of the spine deflection that occurs as a result of the probe advancing.

What follows: Details of the hardware and software you will need in Lab 8T.

Hardware:
ThorLabs DVR001 ($700) Motorized Linear Actuator
(See detailed product information at: http://www.thorlabs.com/NewGroupPage9.cfm?ObjectGroup_ID=1881)
This device, a motorized linear actuator, is capable of linear travel with a repeatable precision of < 1 micron. The motorized actuator has been fitted with a split-tip probe, which allows for precise contact with a single spine. Controls for the actuator occur through a ThorLabs BSC101 controller ($1300) which receives instructions from the main computer. ThorLabs produces associated software for the controller with a simplistic GUI. In our case, however, a LabVIEW program has been written to allow specialized control of the actuator for the purposes of data collection.

Mechanical Cradle
Because the linear actuator has only 8mm of total travel, an adjustable arm has been built (KJM) to hold the actuator/probe in place at an appropriate distance from the specimen. The cradle can be moved vertically by adjusting the height of the supporting lab jack. It can also be moved around two axes of rotation, one at the "elbow" gear junction, using a mechanical pin brake, and the other at the "wrist" junction, by shifting the position of actuator/probe in the vise grip.

[Images needed]

Specimen Platform
The leg preparation is to be placed on a copper platform, which also functions as a ground. The copper has been machined out and filled with a transparent silastic compound which may be penetrated by dissecting needles placed through the cockroach leg. By loosening the knob at the side of the platform, it is possible to adjusting the angle of the platform.

Electrodes:
Paul Waltz has designed and fabricated an electrode holder that positions 3 needle electrodes 2.5 mm apart to penetrate the silastic and hold the preparation in place.

Microscope Camera
The OptixCam camera can be inserted in the right eye piece of the dissecting microscope, and connected to the main computer via USB port. Image and video capture occurs in the OCView associated software, which can be found in the Start menu list of programs.

Software in IP folder...

LabVIEW VI (A): 8T_11_ThorController.vi
LabVIEW virtual instrument (VI) sends commands (either sequenced or instantaneous) to the THORLABS BSC101 controller for the DVR001 linear actuator. All controls are accomplished by ActiveX controls which appear as "Invoke Nodes" in LabVIEW. Each ActiveX Invoke Node takes user inputs in the form of numerical codes and then either "gets" properties from the Thor controller or "sets" properties of the controller, i.e. sends instructions to the linear actuator. For specific information on the function of each Invoke Node, right click the node and consult the Help menu.

Using the VI it is possible to specify the positions of any number of absolute moves, along with the maximum velocity the actuator probe should travel at, and the time the device should wait to initiate the next move. While moves are being completed according to sequencer parameters, the VI program queries the BSC101 controller for its current position several times per second, so as to track the position of the actuator in real time. An array of positions and their corresponding times are saved in a .mat-file over the course of each program execution. These arrays are loaded as variables in the MATLAB program complimentary to this VI.

Trigger functionality of the BSC101 controller is also accessed by the LabVIEW VI. During the second phase of the program, the VI instructs the controller to output a logic HIGH from its trigger I/O pin at the moment when the actuator begins to execute a sequenced move. This logic HIGH can be read by another device or VI to set off simultaneous program execution.

Below is an image of the front panel of the fully functional VI. The arrays at the bottom right of the front panel are controls used to input position and velocity directions to the Thor controller. The Thor panel at the top center of the front panel can be used to give instantaneous instructions to the Thor controller, and so check functionality.

LabVIEW VI (B): 8T_11_PulseRate.vi
This VI (block diagram shows below) is similar to the one used in Lab 8. This VI differs because it collects data over an extended period of time, then saves all data to a *.mat file, which can be loaded in a MATLAB m-file. All data analysis is performed in a MATLAB m-file, rather than in a MATLAB script in the VI. Also different: the VI, once started, waits in a while loop until it detects a logic HIGH from the NI board, at which point it breaks out of the loop and proceeds to collect electrical impulse data. The logic HIGH should originate from the 8T_11_ThorController VI, and indicate that the actuator probe has begun moving. The period of time over which electrical data is collected is specified by a control in the VI front panel.

MATLAB M-File A: analyze_blaberus_8T11.m
All data collected from both VI's is loaded then analyzed in this matlab script. The code for loading saved .mat files is included below. Specifically, the data consists of position data for the linear actuator, and electrical impulse data from the electrodes at the specimen. The rest of code in this file (not shown) plots both data sets and then uses a threshold discriminator to count spikes.

MATLAB M-File B: video_processing_8T11.m
MATLAB's image processing tool box allows images and video to be loaded, manipulated, analyzed, and played back. This m-file, in the image below, uses just the basic image processing tools. It loads the file, the plays it back, and then selects a single frame to display as an image.

Requirements:

Your goal is to assemble a VI + Thor controller to move the probe next to a spine while collecting spike data. The data will be saved for analysis. This will require that you take these steps to get all phases...in phase...

1. Place the specimen on the platform and connect electrodes to amplification system and NI input board.
2. Move the motor with probe into the mechanical cradle; adjustment position of the probe tip with aid of dissecting microscope.
3. Plug in all necessary wires for amplifier and sound system; start the Thor BSC101 controller, and open both LAB8T_11 VI's.
4. Hook-up the trigger, from the Thor controller "Control IO" pins to the NI input board. You will need to consult the following pin diagram to determine which pin to wire to the NI board. Remember to include a reference ground pin wire.

5. Build the VI shown below. Start with the broken default Lab_8T11_ThorController.vi in the IP folder. Add the control arrays. Use the arrays to program the probe to move to a pre-selected absolute position, hold the position for a set amount of time, then return to home. You will have to figure out the basics of how the VI is working to do this. To help you out, we've placed red and yellow signs that indicate where to place the missing arrays controls.

6. Check that the probe is moving as you want it to, both by running the Thor Controller VI and by playing with the controls on the front panel. You can observe the movement of the probe and spine under the dissecting microscope.
7. To run the experiment, first start the 8T_11_PulseRate VI, which will wait in the while loop. Then run the 8T_11_ThorController VI. On user input "YES", the Thor controller should trigger and the other VI should start collecting pulse data. These two VI's running simultaneously will allow electrode data to be collected while the probe is moving as programmed, thereby allowing detailed response analysis. Use the charts in either front panel to check in real time that the experiment is proceeding.

8. Now pull up the analyze_blaberus_8T11 m-file in MATLAB. Run the m-file to check data by plotting.

9. In the m-file you must alter the threshold discriminator to make it a window discriminator, just as you have done in previous labs.

Follow-Up Questions:

1. Using the data collected, relating probe position to afferent response, develop a model relating the position and velocity components of the probe motion to the frequency response from the stimulated spine.

2. Additionally, by applying analytic geometry, determine how the linear motion of the actuator translates to the deflection of the spine.

4-point bonus:

Make a video of spine deflection due to probe movement!

Try setting up the microscope video camera: First line up the dissecting microscope over the probe and specimen, then replace the right eye piece with the microscope camera lens. Plug the camera into the main computer and start the OCView software. Use the OCView software to help you adjust the dissecting microscope and bring the image on screen into focus. To illustrate, I've included a screenshot of the camera and software in action.

Because MATLAB image processing is limited by the computer's available RAM, you should take videos at the lowest resolution possible. Configure the video capture properties and select the lowest resolution.

Start the camera capture, saving the AVI file to the directory of your choice. Remark only, that this must be the same directory from which the video file is loaded in the complementary MATLAB m-file. Next, restart the T_11_PulseRate VI, followed by the 8T_11_ThorController VI. This allows you to collect probe position data, impulse response data, and image data simultaneously.

After re-running the experiment, stop the camera. Open video_processing_8T11.m in MATLAB. This will allow you to play back the video you've just captured.

Super 3 point bonus:

Modify the video_processing_8T11.m code, so that the MATLAB file only plays back the frames that capture the experiment in action, not the dead space on either end.

HINT: To do this you will have to change the inputs to the MOVIE ( ) function. Consult the MATLAB help menu for the function "MOVIE" to determine how to make the edit.