How To EIT

How to use EIT to acquire images

Prerequisites :

First of all you will need the following repositories cloned to your computer from github (this will take a while). If you haven’t set up github yet you can follow the tutorial here.

The ScouseTom repository

git clone https://github.com/EIT-team/ScouseTom  

The Load_data repository

git clone https://github.com/EIT-team/Load_data

The Reconstruction repository

git clone https://github.com/EIT-team/Reconstruction

The Neonate2016 repository

git clone https://github.com/EIT-team/Neonate2016

Make sure these folders are in a drive partition where the user has read/write permissions.

Make sure the folders and subfolders where the matlab functions are located are added to path otherwise the functions will not work

Install Biosemi software

To install the Biosemi software just go to this link download the actiview version compatible with your screen resolution and download the respective Labview runtime engine.

Install the Labview runtime engine first and then install Actiview.

Install Paraview software

To install Paraview software just go to this link choose your OS, click download and then install the program.

Step 1

Components:

• Current Source
• Biosemi + Biosemi DC battery
• ScouseTom
• Switch network
• USB Link
• PC
• Tank Set up the components following this schematic:

Step 2

Matlab Set-up

1. Run

    [ Ard ] = ScouseTom_Init( ArdComPortStr )  
   

Change the ArdComPortStr with the comport the Arduino is connected to.

For example:

 [ Ard ] = ScouseTom_Init( ‘COM4’ )

To find the comport search for device manager as shown here

Note the name of the comport is shown in brackets

2. Load Testing_log.mat which can be found in this folder ...\ScouseTom\src\matlab

Then Run

   [ Ard,ExpSetup,OKFLAG ] = ScouseTom_SendSettings( Ard,ExpSetup)

The current source (Keithely) should display > Settings chk OK

Step 3

Data acquisition

Biosemi

1. Select A32 channels
2. Deselect checkboxes and filters on the left hand side

3. Start new file, name it and select a folder to save it, remember the folder because you will need it later

Matlab

4. Run

   [ Ard,ExpSetup ] = ScouseTom_Start( Ard,ExpSetup)

• note that you don’t need the NoPrompt argument found in the scrip file, thus you can delete it

• You can change the settings sent to the current source by double clicking the variable ExpSetup found in the workspace. For example the default setting for Repeats is set to 1500 you can change it to 10 (for a shorter data acquisition time) by double clicking it, change the number to 10 and then close the window.

• Note that if you already sent the settings to the current source you will have to send them again.

5. A prompt will appear select the yes option
6. Select the file you created with Biosemi
7. Another prompt will appear, don’t press anything go back to Biosemi and click the Pause Save button witch will start the recording
8. Now go back to Matlab and press ok to start the injection
9. After the injection finishes press stop on the top left hand corner to stop the recording.

To record another file just repeat the steps from step 3.

Step 4

Data Processing

Matlab

1. Run

   [ BVstruc ] = ScouseTom_LoadBV( );

2. Select one of the data files you recorded, you will have the same procedure with all of the data files you have recorded

3. The function will create a data file that will look like this Filename-BV.mat, we will use this files in the reconstruction phase

4. Make a new folder here ...\Neonate2016\SerialInj\Recon ex: Yourname_Recon

5. Find the recon_Hadi_Sim.m file in the Neonate2016 repository ...\Neonate2016\SerialInj\Recon\Hadi , rename the file and copy it to the folder you have just created.

6. Open the scrip file

7. On line 4 write between brackets and commas ['...'] the directory where the Jacobian is located.

• If you need more information about the Jacobian please ask someone from the lab

8. On line 7 replace the string with the name of the file that contains the Jacobian
9. On line 32 replace the string with the location of the baseline file
10. On line 33 replace the string with the location of the perturbation file
11. On line 136 replace the string with the name of the perturbation file
12. This scrip will create a .vtk file wich we will use in the Paraview program in order to visualise the data.

Paraview

• On the top left press the open button and select the .vtk file you have just created and click apply

• In order to visualize the data better, multiply the value in the min box and insert it in to the max box

Optional:

• You can adjust the opacity with this image here slider

• You can change DATA to SOLIDCOLOR image here