User Manual v4.

OTBiolab24

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Index
Introduction ................................................................................................................................. 5
PC Requirements...................................................................................................................... 5

OT BioLab24 installation .............................................................................................................. 5

Additional Component ................................................................................................................. 6

Python .......................................................................................................................................... 7

Matlab .......................................................................................................................................... 7

Main Interfaces ............................................................................................................................ 8

Main Menu................................................................................................................................... 8

Setup ............................................................................................................................................ 9

Offline......................................................................................................................................... 11
Track 13

Realtime ..................................................................................................................................... 15

Use cases .................................................................................................................................... 16

Create a new setup ................................................................................................................ 16
Run an acquisition .................................................................................................................. 17
Review a file ........................................................................................................................... 19

Activation Map ........................................................................................................................... 20

Trapezoidal Biofeedback ............................................................................................................ 21

Absolute scale ........................................................................................................................ 24
Relative scale ......................................................................................................................... 24
Start a protocol ...................................................................................................................... 24

Custom Processings ................................................................................................................... 25

Additional script files ............................................................................................................. 26
Custom Processing Panel ....................................................................................................... 27

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Selected processing panel ..................................................................................................... 31

Run selected processing ........................................................................................................ 32

Code Editor ................................................................................................................................ 34

Editor button panel ................................................................................................................ 36

Graph Editor ............................................................................................................................... 37

Trigger Sampling ........................................................................................................................ 41

Matrix Creator............................................................................................................................ 44

Signal Processing ........................................................................................................................ 46

Absolute value........................................................................................................................ 46
Average Rectified Value - ARV ............................................................................................... 46
Epoch Average ....................................................................................................................... 46
Mean Square .......................................................................................................................... 46
Max Min Mean ....................................................................................................................... 46
Root Mean Square - RMS ....................................................................................................... 47
Signal-Noise Ratio - SNR......................................................................................................... 47
Filtering .................................................................................................................................. 47
Median Frequency - MDF ...................................................................................................... 48
Mean Frequency - MNF ......................................................................................................... 48
Fast Fourier Transform - FFT .................................................................................................. 48
Power Spectral Density - PSD................................................................................................. 49
Average .................................................................................................................................. 50
Coefficient of Variation - CoV ................................................................................................ 50
Binarization ............................................................................................................................ 50
Linearization and Parabolic .................................................................................................... 50
Standard Deviation ................................................................................................................ 50
Band Pass EEG ........................................................................................................................ 51
Calibration .............................................................................................................................. 51

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Convolution ............................................................................................................................ 51
Derivative ............................................................................................................................... 52
Envelope................................................................................................................................. 52
Integral ................................................................................................................................... 52
Sum 52
Activate Instant Detection - AID ............................................................................................ 52
Find Zeroes ............................................................................................................................. 54
Normalization......................................................................................................................... 54
Time Shift ............................................................................................................................... 54

Decomposition (coming soon) ................................................................................................... 54

EEG Impedance Check ............................................................................................................... 55

Troubleshooting ......................................................................................................................... 56

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Introduction
OTBiolab24 is a software developed by OT Bioelettronica, completely free and downloadable at:

https://otbioelettronica.it/en/software/

It allows to acquire signals from OT Bioelettronica devices, review and process them. It has been designed
for .NET Core and Windows 10 operating system with 64-bit processor resolution and use WPF
technology to design the graphical interface.

For a best experience we recommend a 1920x1080 resolution monitor.

PC Requirements
Operative system: Windows 10
Processor: Intel i3 5th generation.
Port: USB2.0 and Ethernet
Hard Disk: 1 GByte for software installation, additional space is required in order to store data and
interact with the database, or the python features
Minimum RAM: 4 GBytes

The minimal PC requirements listed allows the proper acquisition of all 256 channels of Quattrocento
equipment (with max sampling frequency 10kHz). The increase of the number of visualized channels can
produce a visualization latency or an intermittent visualization.

OT BioLab24 installation
OTBiolab24 installation procedure requires few minutes and allows to install the software. Download the
installer and run it. The start-up window will appear, showing the software is under copyright law and
then asking the user to select the installation folder.

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To confirm the installation the user must allow the software to apply changes to the computer, otherwise
the procedure is reverted and OTBiolab24 will not be installed.

Additional Component
The new OTBiolab4 provides the possibility to create, run and import custom codes written in Python or
MATLAB. In the default installation the necessary components are not automatically installed and require
a specific procedure to start using it. The following page is the view dedicated to these procedures.

Let’s focus on python and MATLAB installation procedures.

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Python
In the python settings the user will be able to start and check the necessary external components to run
custom codes. To run python in a computer an interpreter must be locally installed and must be pointed
through the “Interpreter” path. If you already have installed python in your computer, click the “Browse”
button and search for your “python.exe” file. If you don’t have python, the installation procedure, that
can be executed through a bat file contained in the software hidden files executed with “Install” button,
will download all the python components, included “python.exe”, and a first list of default python
processing created by OTBioelettronica. The default path of interpreter and of processing folder are
reported in the dedicated textbox and can be changed through “browse” button.

With the “Check” button the software will verify if the interpreter path exists and if the processing folder
is valid. If the check is overcome a green tick will appear near “PYTHON SETTINGS” title, otherwise a red
cross will be showed, and the involved path problem will be highlighted through a red box. Below an
explicative image of both situations:

So for a proper installation, click the “Install” button and verify the components with the “Check” button.
If something goes wrong a dedicated message will be showed which advise the user to run the installation
with administrator permission.

ATTENTION: this installation procedure is totally automatic, for this reason a huge amount of
components are installed, pay attention because it will require 1.8 GByte of free space. The installed
environment can also be used and updated with “Miniconda3” software if installed in the computer.

Matlab
In the MATLAB settings subsection, the user can find a dedicated textbox for the default MATLAB
processing, an install button and a check button. The textbox contains the path to the folder which should
contain the default MATLAB processing. For MATLAB, the installation procedure is simpler compared to
python because just the default processing developed by OTBioelettronica are downloaded in a
dedicated folder. The “Check” button just verify that the default MATLAB processing folder exists and is
a valid folder. The result of the check will be showed in the same way of python (green tick or red cross).

ATTENTION: the installation procedure is really simple and just processings are installed, this mean that
if the user hasn’t MATLAB already installed in the computer, the software will not be able to run MATLAB
processing. The check doesn’t verify the installation of MATLAB, so be careful to this aspect.

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Main Interfaces
This chapter described the main windows the user will encounter during a classic utilization of
OTBiolab24.

Main Menu
This is the main menu. It’s divided in two sub-section: tools and analysis.

Tools contains three different buttons:

- Database Management: it takes the user to the database window where he can interact with
the database to organize his work. He can create new subjects, new studies and place the data
in a tree structure in order to easily access file and handle large amount of data and information.
- Community tools: this window contains many tools created by the EMG community that are free
to use. Most of these tools can be used with Matlab or Python.
- Option/Support window: contains OTBiolab24 configuration parameters such as specific path
for features.

Analysis contains three different buttons:

- Realtime: this window is specific to the realtime acquisition, where a user can select a setup,
visualize signals from the device and start a recording.
- Offline: through this window it can be possible to open a recorded file, visualize the signal, run
processing and do other kind of operation.
- Setup: this is where the user can create a device setup. Each setup specifies the device
configuration during the realtime acquisition (number of channels, sample frequency and other
hardware parameters)

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Setup
The setup window contains a 3D visualization of each device. From the left side menu, it’s possible to
select the device for which we want to create a setup and see its 3D model. It can be possible also to
move the model in a free visualization mode and zoom in and out for details.

When the device is selected the device aside list switch to the adapter list of available adapters for that
specific device. In the following picture a list of Quattrocento adapters is displayed.

Using mouse drag and drop the user can place the adapter in the corresponding slot and then fill it with
the sensor in the right-side menu. In case the device has a back panel, the user can access it with the
dedicated button and move between the two figures. The 3D visualization automatically rotates to
visualize it.

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The back panel button visualize the AUX connectors and switch the left side adapter list with the AUX
sensor list. The user can configure an AUX connector in the same way on other slot: using mouse drag
and drop.

OTBiola24 allows to create and save multiple setups. To see and pick one of them the user can use the
toggle button and switch to “Load Setups”. In this way the left list of device switch to the list of saved
setups.

A saved setup can be selected to see the current configuration.

The setup window provides a set of buttons to access specific feature:

- Complete: confirm the setup completion and add to the list of saved setups

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- Place Electrodes: open a new window to specify muscles where the electrodes are placed
(currently unavailable)
- Clear: remove all adapters and configuration from the visualized setup
- Go Back: use this button to go back to Main Menu.

Offline
The offline window is used to open file, visualize signals, run processing and much more. It’s composed
by two side vertical menus and a central part dedicated to the soundtrack, a graphical container where
the tracks are displayed. On the left side a vertical menu contains different buttons to access additional
features and open sub-menus. On the right size the space is dedicated to those sub-menus. Based on the
selected buttons on the left a different sub-menu is opened on the right, containing many other buttons
or controls depending on the selected functionality.

To navigate the data in time it’s possible to use a set for dedicated buttons placed in the bottom left part
of the soundtrack.

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These buttons are used in this order to: increase the horizontal scale (zoom in), decrease the horizontal
scale (zoom out), zoom to a specific selection of time and fit the entire track length in the window. Right
to this section there is an horizzontal time bar that display the current visualized range of time a include
a scrollbar to move along it. A set of white vertical lines are used as time separator for the x-axis.

The left side menu of the Offline window is composed by a set of buttons that enable features.
The buttons are:

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- Open File:
Use this button to open the right-side menu where you can select to open a new file,
open a file from the database or open a recent file.
- Import File:
Use this button to open a dialog window and select a file to import. Differently form
the open file, the import, will keep visualized current file without overwriting the
soundtrack content.
- Save:
Use to save the file on disk.
- Processing:
Use this button to open a right-side menu containing the OT Bioelettronica processing
suite. Check future chapter for the entire list of processing and its description.
- Python Processing:
Use this button to open a right-side menu containing the OTBioelettronica python
processing suite. This is where you can also import a custom processing or implement a
new one.
- Graph Editor:
This button opens the Graph Editor, a GUI specialized in python processing pipeline.
- Video:
Open the Video window.
- Marker:
Open the Marker window.
- Export:
This button open a right side menu where you can select the export format (Matlab .mat,
Csv .csv, Python .npy)
- Group Tracks:
This button is used to group together different track into a Grouped track.
- Ungroup Tracks:
This button is used to separate a grouped track into single tracks.
- Edit Tracks:
This is a toggle button that can be turned on or off. If this function is activated, a scissor
image will substitute the mouse arrow, and the user will be able to remove track pieces
from the visualization.
- Settings:
Open the setting right-side menu.
- Go Back:
Use this button to go back to the main menu.

Track
A track is the graphical representation of an acquired channel (or more than one). It shows information
about the name of the channels, the acquisition configuration such as sample frequency and conversion
factor, and it loads the data from file to display them. A track that contains multiple channels such as all
channels of a matrix is called grouped track.

A set of buttons is associated to each track and are used to:

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- Set title: change the track title.

- Show points: data are visualized as interpolation of point. Enable this to see values as red dots.
- Manage selections: open a little menu to handle the track selections.
- Display information: this buttons open a sub-windows where all the information related to the
track are displayed. Such as hardware configuration used during the acquisition, source track
conversion factor, etc.
- Show vertical lines: display a set of vertical lines.
- Open the free hand modes: open the track in a new window where it’s possible to zoom in and
out the values and move along the track using mouse wheel and other shortcut.
- Vertical Zoom In: increase track vertical scale.
- Vertical Zoom Out: decrease track vertical scale.
- Autoscale: Load max/min value of the visualized data and set them as vertical scale.

In the track right part there is an additional vertical menu with another set of features, more complex
than the previous and that allows a deeper kind of personalization.

The buttons are:

- Choose channel to plot: turn on and off channels in the grouped track. This feature make sense
if the grouped track is the representation of a matrix and the user wants to remove specific
channels from the visualization.
- Choose color: open a window that allows the user to change color of track data and background.
- Set vertical range: specify the min/max values for the
vertical scale. It’s also possible to remove the vertical
offset in case of a grouped and visualize all the track on
the same level.
- Shift: using a slider it’s possible to shift to the right or
left the track adding zeroes sample to the data. The file
containing the original data is not modified.
- Reset: reset changes to default and display the original
track.

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Realtime
The realtime window structure is very similar to the offline ones but it contains a slightly
different set of buttons and features.

This window is meant to be used selecting a setup of the device we want to acquire with and
then starting the acquisition. The start button sends a start command to the device and then
the software begins to receive data packets and distribute them to the tracks. The data are
drowned with a specific time range and overwrite the old ones on the window.

The realtime buttons in the realtime menu are:

- Processing:
Use this button to open a right-side menu containing the OT Bioelettronica processing
suite that can be used during a realtime acquisition.
- Video:
Open the video window.
- Marker:
Open the marker editor.
- Activation Map:
Open the activation maps processing window.
- Trapezoidal Feedback:
Open the trapezoidal feedback window.
- Setup:
Open a right-side menu where to select the setup to use for a realtime acquisition.
- 3D Inertial Visualization:
Open a window specific to the 3D visualization of devices with quaternions in order to
see the direction and orientation of the device.
- Start:
Use this button to start and stop the acquisition. A setup must be selected in order to
do that.
- Pause:
Use this button to pause the acquisition and freeze the visualization.
- Record:
Use this button start and stop recording data on a file.
- Settings:
Open the setting right side menu.
- Go Back:
Use this button to go back to the main menu.

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Use cases
This chapter describes a series of use cases that contains the main features of the software. Those cases
are examples of main functionalities and what can be done using OTBiolab24.

Create a new setup

This step is necessary in order to acquire signals from an OTBioelettronica device. Creating a setup means
specify the configuration of the device before starting an acquisition. The setup window can be opened
from the right-bottom button of the main menu.

Then the setup window opens and from the left side is possible to select the device. Each device has
different configuration, please refer to the device user manual for additional details. As example the
Quattrocento will be used for this use cases.

Using the mouse it’s possible to drag and drop an adapter into a connector slot. If the adapter can be
placed in that specific connector the slot turns green, otherwise the red color appears and it’s not
possible to insert it there.

By clicking on the connected adapter, a right-side menu opens, allowing to insert a sensor. This is done
as previously using the mouse drag and drop.

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The user can proceed this way and configure all the
connectors he needs and when it’s done, click on
Setup Complete button to save the setup.

Run an acquisition
One of the software main goals is to acquire, save and visualize data from OTBioelettronica devices.
Supposing that the user already has created a setup (refer to previous use case) it’s now time to start the
acquisition.

From the main menu click on the top-right button to enter the realtime window.

As described in the related chapter the window contains a vertical menu with many options and features.
What we need to start an acquisition is to select the setup we want to use.

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Of course, we consider the device to be turned on and connected to the computer.

To select a setup, click on the following button to open a right-side menu.

The entire list of saved setups is shown, and the user can pick one of them. A recap of the
configuration is displayed to summarize the setup information and details.

Then, click on the orange Start Button from the left side menu to run the acquisition. Based on the setup
the tracks are created and displayed in the center part of the window. For each connector a specific
grouped track or single track is created, this difference depends on the number of channels contained in
the connected sensor. It could be possible that additional control channels of the device are shown too.

The start button is substituted by the Stop Button and it’s now possible to record data on a file while the
acquisition run. Click on the record button to start the recording. The icon turns green, starts blinking
and a timer is displayed.

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When the recording is complete, click on the green tick icon to save a file.

Review a file
Using OTBiolab24 is possible to open a .otb4/.otb+ file, visualize the recorded data and use a large set of
tools to analyze, extract information or export them. Each use is specific to the user’s goal and this use
cases cannot cover all of the different feature but to provide an example of file opening.

From the main menu click on the center-right button to enter the offline window.

Click on the top-left button to open the right-side menu dedicated to files. It contains two buttons used
to open and import and also the list of recent files, to give quick access to most recent data.

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Click on Open File button and select a file using the dialog window. Then the software will load the data
and create the list of tracks.

Using the following buttons is possible to change the horizontal scale of the file and set the favourite
level of zoom. Then with a horizontal scrollbar the user can move along the time and look at the signals.

A vertical scrollbar is provided too to move along the tracks.

In case of grouped tracks is possible to separate them using the dedicated “-” green
buttons. Viceversa it’s possible also to group many single tracks into a grouped track using
the “+” button.

Activation Map
The activation map is a tool included in OTBiolab24 that allows to visualize the signals as a heat map,
respecting the grid shape and place many grids side by side to replicate the acquisition.

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The activation map window can be found in the offline window inside the Processing tab called EMG and
it’s composed by:

1) A list of tracks: the selected tracks are displayed here together with their grids (if possible) as
buttons to be inserted in the center part. With mouse drag and drop is possible to place them in
the middle. Only group track can be visualized in this tool for obvious reason.
2) The ARV slider: this slider is used to determine the time window of the ARV calculation.
3) The map color slider: this slider is used to set the minimum (blue) and maximum (red) values
that will be used to display the heat map. Adjust the values accordingly (max, min values of the
data)
4) The heat maps: the activation maps representation. Is possible to place multiple grid side by side
in row-column visualization.
5) Horizontal scrollbar: used to move along time.

In order to prevent very quick value changes due to EMG data characteristic, the activation map doesn’t
display raw data, but the Average Rectified Value (ARV) is calculated before passing them to the graphical
interface. The ARV value is calculated with a time window that can be changed using the slider and goes
from 0.5s to 1.5s

A realtime version of the activation map is available from the realtime window, by clicking
on the following button. In this case the ARV is not calculated on a specific time window
but on each single packet of device data.

Trapezoidal Biofeedback
The Trapezoidal biofeedback is a specific tool used by many researchers out there in the previous
OTBioelettronica software and for this reason it has been implemented in OTBiolab24 too. The main
purpose is to define a specific path and, based on the subject maximum voluntary contraction (MVC),

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make the subject to follows it during an acquisition. In order to do that, a specific window has been
implemented and it’s accessible from the realtime window, using the following button:

It’s possible to run the trapezoidal biofeedback on a grouped track (a track that contains multiple
channels) and in this case an additional information is requested.
If so, the software asks the user to specify whether he prefer to calculate a mean of all channels and
using it to follow the path. Otherwise he can specify to calculate the differential between two particular
channels. With this solution, at each time instant, the software will calculate the difference between
values and this difference will be used to follow the path.

This choices is possible by clicking on the related toggle button.

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The displayed windows contains different controls that allows to add a scale factor for the data (very
important if the customer use a load cell), record the MVC or write it manually, enable or disable the
visualization of a specific channel (multiple channels can be visualized in the trapezoidal feedback), zoom
horizontal scale, set relative or absolute scale, open the setting to create a path and start or stop the
protocol.

Creating the trapezoidal path is one the most important feature in the trapezoidal biofeedback and to do
that a separate window has been developed. Using the Settings button it’s possible to open it.

Through this graphical interface a path can be defined and saved along with the others and chosen from
the user for the trapezoidal feedback. To create a path, it’s possible to insert point by point or sinusoid
from the left menu. It’s possible to manually edit each single point values (x, y) from the right side list
and also to swap position of two different point by clicking and dragging them.

Using the related button is possible also to manually click on the graph to insert a point.

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When the settings window is closed the path will appears in the trapezoidal feedback window graph.

Absolute scale
The absolute scale displays the data of the track in the graph, the same values displayed in the real-time
plotter window. In this mode it’s possible to record the MVC, specifying the timer duration.

Relative scale
The relative scale changes the vertical scale of the graph and adapt the values accordingly. This scale set
the MVC as the value 100 of the graph and it’s used to display % of MVC in a 0-100% vertical scale.

Start a protocol
The trapezoidal protocol is the intended use of the Trapezoidal feedback and can be accessed following
these steps:

1) Create a path using the setting window.

2) Write or record the MVC, this is mandatory in order to have the correct vertical scale.
3) Switch to Relative scale.
4) Start protocol.

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Custom Processings
The software allows to run MATLAB and python script in an easy and intuitive way. From the point of
view of software, a custom processing is a simple folder system with files written in python or MATLAB
containing different code lines. The main folder of a custom processing gives the title to it, and inside of
it there are other folders containing the different step of the processing. Every step can be written either
only in MATLAB or only in python, but inside of a processing there can be different steps, this mean that
a processing is a chain of steps, where these can be all python steps, all MATLAB steps or python and
MATLAB steps. This structure is mandatory to import a processing inside the software, and every step
needs to contain a “main.py” file for python steps, or a “main.m” for MATLAB steps. In the next chapter
called “Graphic Editor” we’ll also see how this structure can be used to merge different processing by
chaining the steps of each one inside a “merged processing”. Here a resume images of processing
structure:

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As you can see from the images, the “00_Python Example”/”00_Matlab Example” steps are identified by
a number which represents the execution order, in case the processing contains different steps. Give a
look to the files contained in the step folder, the “main” is the file that will be mainly updated by the
user, it’s the script that contains the main elaboration. The other files provide different functions to
interface the script with OTBiolab24 software and will be fully explained in the next sub-chapter.

Additional script files

The main feature of the custom processing is the possibility to run your custom scripts by selecting data
from OTBiolab24 software and plot the results and visualize them in OTBiolab24. To create this bridge an
interface library has been developed and added to the custom processing, if the user wants this type of
feature it needs to be integrate in its own script. This library has been built with different files and from
a first point of view seems to be different between MATLAB and python steps, but the functionalities
provided are exactly the same and can be generally grouped in “Classes” and “Interface functions”.

1. CLASSES: the classes used by this library are included in OTBClasses.py file and Channel, Section
and Track files for MATLAB. The programming language is different, but the concepts are exactly
the same, indeed in the OTBClasses.py file the same classes are defined and included. This
explanation is meant for all those who want to update the classes and insert new methods or
properties to create more complex algorithm, actually the only purpose of these is just to have a
simple container to access the data.
a. Channel: this class represents the data contained by each channel of the track. Inside of
it there is a simple property which contains a list of double values.
b. Section: this class represents the section selected in the track of the software. When you
decide to select just one or multiple pieces of a track, this is translated in section class,
one for each selection the user did previously. Inside the section class there are a start
double value, representing the beginning in seconds of the selection, an end double

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value, representing the end in seconds of the selection and a list of channel objects which
contain the data.
c. Track: this is the more complex class compared to the other and represents a
python/MATLAB copy of the track used inside OTBiolab24. Inside of it are defined, a title
field, a string representing the track title of the software, a unit of measurement field, a
string representing the unit of measurement of the initial track, a frequency field, a
double value representing the sampling frequency, a number of channels field, an int
value representing the number of channels included in the tracks, a device field, a string
representing the device name used to acquire the signals, and finally a List of Section to
access the data. There also different methods defined that can be used to interact with
the main software after the processing execution.
SaveData: this method requires a path and a track index to create a file “.data”
containing the data with a unique name. This file format will be highly explained in the
chapter “Run selected processing”.
SaveText: this function takes a path, a track index number and a channel title string as
input. It creates a “.text” file where the data contained in the track are saved in a text
format by adding for each channel the channel title specified as input. The file will be
saved to the patch with a unique name created by track index number. This file format
will be highly explained in the chapter “Run selected processing”.
GetDataFromSections: this function takes as input the index of a section and returns a
matrix containing the data contained in that section.
Plot: this function creates one plot for each section contained in the track.
2. INTERFACE: the interface part is managed through different functions which use the classes to
communicate with the main software. There are different functions inside of it, and the main are
explained below:
a. OpeningOTBPlusFile: this function receives a path to otb+ file and returns the list of
tracks loaded by this file. The track type is defined in the Class explanation.
b. OpeningOTB4File: this function receives a path to otb4 file and returns the list of tracks
loaded by this file. The track type is defined in the Class explanation.
c. LoadDataFromXXFolder: this function is used to read all the “.data” files contained in the
Common Folder and returns the list of tracks, one for each file, as output.
d. WriteDataInXXFolder: this function gets a list of tracks as input and call for each one the
method SaveData explained before. Each track will create a “.data” file inside the
common folder that can be used to another processing or used by the software to plot
the data.
e. WriteMessageInXXFolder: this function gets a list of tracks as input and call for each one
the method SaveText explained before. Each track will create a “.text” file inside the
common folder that will be used to create a message box in the software.

ATTENTION: apart the main the other files are totally different between python and MATLAB and need
to be modified with extreme attention, because it can influence the proper script work. These files are
automatically generated by the software when a new processing is created but the only mandatory file
in each step is the “main” file.

Custom Processing Panel

To open the Custom Processing menu the user needs to click the button called “Custom Processing”:

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This will open the list of the current custom processing saved in the software in the right-side menu. If
this list is empty means that you missed to install the necessary components to run python/MATLAB
script, follow the “Additional Components” chapter to see how to handle it. If the user has installed both
python and matlab tools, he should be able to find the default python/matlab processing installed during
the procedure.

2) Buttons Panel

1) Processing List

3) Processing Categories

The processing list is filled with the processing actually found in the software folders specified in the
“Settings” View (see chapter “Additional Components”), this includes the default Matlab/Python

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processing and the new processing created or imported by the user. Each processing is classified with a
category, that can be used to filter the processing list by clicking in the “Processing Categories” bar. Each
category is a button which selects the processing under that specific category. The “Buttons Panel” allows
user to interact and update the processing list, below a full explanation of the different buttons:

1. Create New Script ( ): With this button the user can create a new processing to add in list. This
feature needs to be used when the user wants to create its own script with its own code. We will
see the entire workflow in the next chapter. The window related to new script tool is the
following:

The processing title is the only mandatory field, the others are set default if the user doesn’t digit
nothing. The category is the same field used by the “Processing Categories” panel. If this category
is the first one, it will be added to the list automatically. If no category is specified in this window,
the “CUSTOM” category is used as default. The description is a simple descriptive field of the
processing, if it’s not added, the “ – “ character will be used. The “Import OTB Library” checkbox
is simply used to create a basic template of the new processing, if this is toggled a basic structure
template with a default elaboration is added to your processing, if not a total empty main file
will be used. The last toggle is used to select if the user wants a python or a MATLAB processing.
When the “Insert” button is clicked the folder representing the new processing is created, and
all the necessary files are moved in it with a dedicated step folder and a main file with a different
template depending on “Import OTB Library” checkbox. The generated templates are quite
important to use all the functionalities provided by the main software, indeed the software
shows different information of the scripts that need to be placed in specific code blocks to be
found and captured. This information is the CATEGORY, the DESCRIPTION and the PARAMETERS.
Here the images and the explanation of these blocks:

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When the processing is loaded and in the main file there is this type of block (left python, right
MATLAB), everything that will be written inside the limiters and under the “DESCRIPTION” word
will be used to fill the description in the Selected Processing Panel.

When the processing is loaded and in the main file there is this type of block (left python, right
MATLAB), everything that will be written inside the limiters and under the “CATEGORY” word will
be used to fill the category in the Selected Processing Panel. If the category has not been found
between the processing contained in the processing list, a new category will be added. This
category can be used to filters the processing list as described in “Custom Processing Panel”
chapter.

When the processing is loaded and in the main file there is this type of block (upper python,
lower matlab), all the lines that are not comments will be parsed to find parameters and variables
to be used and showed in the Selected Processing Panel. This block is overwritten in the code if
the parameters are changed from the software interface and will be substituted in the software
if the code is changed from the editor and reload. The variables that can be parsed and
recognized are int, double, float, string, char and bool.

ATTENTION: The collections are not recognized as type, so if you write a list in the parameters
block it will be recognized as string.

2. Import Processing ( ): With this button you can import an existing processing to your list and
use it like the other processing. The software does different checks about the processing folder
structure, that needs to be exactly the same to the one described in the introduction, and the
presence of main files in the different steps of the folder. The best solution to add your code in
the custom processing list is creating a new processing and moving your files inside the step 0
folder by renaming the main file as “main.py” or “main.m” depending on the script language.

3. Export Signal ( ): the export signal functionality it’s a really important feature for all the users
that want to develop their own code. As we’ll see in the next chapters, the software provides a
simple text editor to visualize the custom processing codes and update them with a lot of
simplification. Obviously, this editor is not a true IDE like MATLAB Ide, Spyder or PyCharm, since
it doesn’t provide debugs instruments or other mandatory functionalities for code development.

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For this reason, OTBiolab24 provides to user the possibility to develop its own codes but using
the signals and the data visualized in the software. The communication between main software
and custom scripts is done through specific files created before the run event, and that need to
be loaded by the script to have the data to elaborate, this allows to run the custom processing
on the signals visualized in the software, and to visualize subsequently the results of the
elaboration. The support files generated by the software in the custom processing folder contain
all the functions to load and write these data, and the data loading and writing are already
written in the main template, in this way, if the processing is created and opened with its
dedicated IDE, it will work if the proper data file will be found in the proper folder. This can be
done through the Export Signal function, just select the tracks that you want to use in the
processing, click the button and the files containing data will be moved in the proper folder, now
the new custom processing can be opened and, in the main file with the support functions of the
template, the user will be able to run the processing with OTBiolab24 data in any IDE.
4. Refresh Scripts ( ): since the custom processing are simply folders with files inside of them,
the user can also manage them through operating system or other software, with this button the
software reloads the processing from the proper folders, in this the external updates can be
transposed to the software.

Selected processing panel

From the processing list you can choose one of the custom processing and it will be opened in the right-
side menu. Let’s see an example:

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In the processing panel there will be a list of steps contained in the processing (in this case just one), with
a description of it (when the user creates a new processing, the description of the windows is used as
description of the first step, see Chapter Custom Processing Panel), and a list of parameters that can be
changed by the user. In the button panel new buttons that manage the selected processing will be added,
below a complete description of these ones is reported:

1. Open script editor ( ): As described in the previous section, the custom processing are simply
folders which contain matlab/python script. With this button the user can open a simple text
editor to visualize and modify the codes. It will be fully explained in the next chapters.
2. Open project folder ( ): this button opens the processing folder in a folder dialog window. This
can be useful if the user wants to manage directly with the files contained in the processing.
Remember that after changes you need to reload the processing with the “Refresh scripts”
button previously described.
3. Export processing ( ): this function will create a copy of the processing folder in a destination
chosen by the user through a folder dialog window. It can be useful to update or create a new
processing starting from an existing one without touching the original.
4. Delete processing ( ): this button is used to delete a processing and remove it from the
processing list. For this function a distinction between custom processing is necessary. The
processing installed with the “Install” function previously described, are called “Default Custom
Processing” and these cannot be deleted or updated in the software. Indeed, in this type of
processing this button is disabled and cannot be clicked. The processing created by the user are
called “User Custom Processing” and these cannot be deleted and update through OTBiolab24.
To distinguish the two types of processing a symbol in the high part of processing button has
been inserted.

(Default) (User)
Other differences are in the editor page, but these will be fully explained in the dedicated
chapter.

Run selected processing

In the final part of the processing panel the start button can be used to run the processing (chain of steps)
in the tracks selected by the user in the plotter view. The software and the scripts communicate each
other through specific files created before the processing is executed and by reading the results in other
files when that processing is concluded. This file exchange is done in a specific shared folder located at
“C:\Users\%CURRENTUSER%\AppData\Roaming\OT Bioelettronica\OTBiolab4\FileToProcess” folder.
When the processing is started different files are generated with different extension:

1. .data files: these are binary files which contain the data and all the information related to a
specific track. Indeed, for each track with at least one selection one file of this type is created.

The first part of the file is a sort of header that contains, track title, sampling frequency, number
of channels, unit of measurement, after the header there are data divided in sections depending
on how many selections the user has done before running the processing. For each selection the

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start time and end time of it are written in the file, and after these the data are saved in double
format, this means that from the script point of view there is no need of conversion. This section
logic is iterated for all the sections of the user. The title is associated with a number to create a
different file for each selected track.

2. .common file: this file is created to resume the files path involved in the processing. It contains
a list of otb+/otb4 that are currently opened when the run button has been clicked.

These files are necessary to communicate with the scripts, and from the script point of view the user can
decide to directly open the files by using the .common file or create a copy of the tracks in the code by
using the .data files. If the scripts want to plot the results in OTBiolab24 needs to create files in a similar
format, in this way the software will check the same “FileToProcessFolder” and will show the results in
different way depending on the extension of the files. The files can be “.data” like before, in this way the
software will create a track for each file and will add this on the current tab, or “.text” files, which are file
that can be created as result file and which are visualized in a message box of the software. So, by cleaning
the “FileToProcessFolder” and exchanging “.data” files the processing can be chained to multiple steps
and obtaining a result viewable in OTBiolab24 software. Here a schematic resume of this process:

OTBiolab4
software

WRITE TO

WRITE TO Common
Folder

Script
step READ
FROM
Is this last
processing step? READ FROM

OTBiolab4
software

As can be seen in the figure, the software starts the processing by writing the selected track in “.data”
format inside the common folder and then the different script steps are executed by repeating the
operation of reading from common folder the data and overwrite the results to common folder until the
steps are all executed. At the end the software does one last reading from the common folder and
translated the .data files in tracks which will be showed in the proper page. The software in the last step,

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will check for the files contained in the common folder by reading them and depending on the data
format it will be manage them in different way. Here a list of the possible files:

1. .data files: same as the previous description. If the software finds this type of files inside common
folder at the end of the processing, it will translate these data in tracks that will be showed in a
dedicate page.
2. .text files: this file is a binary file which can contain processing results. If the software finds this
type of file, it will create a message box that contains the results written in .text file like a message
string.

Code Editor
As described in the “Selected processing panel” chapter, through the button “Open scripts editor” the
user can open a text editor to visualize and modify the codes contained inside the processing folder. The
editor will automatically recognize if the files in the steps are python or MATLAB and a view with
dedicated buttons, syntax highlights and functionalities will be opened. Here the images of editor opened
for MATLAB and python steps:

Main tab to
change
processing steps

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Secondary tab to
change
visualized file

We are visualizing a User Custom Processing that involves two steps, the first one written in python and
the second one written in MATLAB. As we can see, the theme is different in the two steps, python code
has a dark theme while the MATLAB code has a white one. Furthermore, the correspondent syntax, like
comments and keywords, is loaded by the editor to highlight specific text pieces like comment and
keywords. The editor provides a “Main Tab” control to visualize the codes of the different step. Then a
“Secondary Tab” control is provided to switch the codes and moving inside the step processing codes
contained in the correspondent folder. Below there is the “Output Console” where different messages
are showed in different colors:

1. Green Messages (Software information): This message represents a normal information of the
software, like the scripts saving, or what script is running at the moment.
2. Yellow Messages (Warning): This message represents a software warning that it’s not blocker.
This type of message needs to be investigated and for the proper processing execution is better
if no warnings are showed. The classic message of this type is the warning that tells user that the
script cannot be saved because it’s a “Default Custom Processing”. Indeed, the default processing
cannot be modified and for this reason cannot be saved by the software.
3. Red Messages (Errors): This message represents a potential error found during the current script
execution. This message, despite the others, is related to script working and not to OTBiolab24.
If a red message is visualized the script is failed, the message will provide you all the necessary
information to understand the script problem and solve it.
4. White Messages (Output): the software get all the output generated by the script, like “print”
functions or the standard channel output of a matlab script. This output is represented through
this white message.

Near the Secondary Tab, there are two buttons with different purposes. The first one ( ) is used to
create a new file called “Untitled” of extension .py if the focused step is Python or .m if it’s MATLAB. The
file will be opened with a “*” in the name tab, that means that it’s never saved, so the first time that the
user run the step or the file, a file dialog will be opened to confirm the name and the path of this new
file. The second one ( ) needs to refresh the step content. In a previous chapter we described the

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processing as a chain of steps represented by folders, so the user can manage them also with other
software or just with operative system by moving files or changing folder names and so on. This button
is necessary to reload the content if this is changed out of the software. This can also be used if the user
wants to remove some files in the processing, he can open the processing folder, remove the files he
wants and refresh the content with this button.

Editor button panel

In the upper part of the editor there is a panel containing different buttons that allow the users to save
and run codes. Here the buttons functionalities:

 Run all steps ( ): this button run all the steps starting from 0 in increasing order. In each
step, the code focused on the Secondary Tab will be executed. Before each execution the
code is saved (if possible, remember that Default Processing cannot be modified/saved) and
then executed. For each executed code, a message containing saving information and
current code title is showed.
 Run single code ( ): this button executes just the code actually visualized, so a precise
script contained in the step actually pointed from Main Tab. The script executed is chosen by
the user, it will be the main code just if the user is visualizing the main code. Remember that
before execution the code is automatically saved, and the info message will be showed in
output console.
 Save ( ): this button can be used to save the specific file actually visualized. This will
generate a message about the success or failure of the saving.
 Save all ( ): this button repeats the Save operation but for all the files contained in all the
steps of the processing. A dedicated message will be showed in the console for each file
saving.
 Open Folder ( ): this represents the redundant functionality of opening the processing
folder. Can be useful if the user wants to change some file name or add other files in a file
explorer window and reload the processing content with the “reload” button previously
described.

ATTENTION: if the user update or add some parameters in the code editor and save the modified files,
to find the same updates in the Processing Panel List, the “refresh scripts” button explained in the chapter
“Custom Processing Panel” need to be clicked.

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Graph Editor
The graph editor functionality can be used just in combination with custom processing developed in
MATLAB/Python codes, this means that at least the installation procedure of python components or
MATLAB components or both, showed in the “Additional Components” chapter, must be completed.
Once that the python/MATLAB components have been installed, the graph editor functionality can be
used. The base concept of this tool is the folder structure of the processing and the step chain contained
in it, indeed since the processing execution can be seen as a cycle operation of read-elaborate-overwrite
in the same common folder, the graph editor allows user to merge the steps of different processing by
creating a new one with the initial steps chained one after the other. To open the graph editor, the user
needs to click the following button of the left panel menu:

A new view will be opened and added in the main docking of the platform:

The main components of this page are the processing list in the left, the graph in the middle, the manage
panel below and a details section that is not visible, but it will be highly explained in the next chapters.

Processing list: it contains all the custom processing, both the default ones added with the installation
procedure and the ones created, added, or imported by the user. In the higher part of the list there is a
field called “Category Filters” that can be expanded by moving over it with the mouse, like in the image
below.

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The options contained in it are the single categories found in the processing list and can be used to filters
the processing list. The options inside this container can be activated or deactivated, when no categories
are activated all the processing will be showed, when one category is activated all the processing which
share that specific category will be showed. The user can select more categories and all the processing
that share at least one of the activated categories. The processing inside the list is draggable elements,
this means that the user can click on a processing and drag it to the graph in the center.

Processing graph: As can be seen in the image there is a graph with a single node called “Insert” placed
in the center of the view. The “Insert” node can interact with the dragged processing, and if the user
leave the mouse when the processing has been dragged over the node, it will be inserted in the graph as
first node, like showed in the figure with the ARV processing.

As can be seen in the image a new “Insert” node appear after the “ARV” node and can be filled in the
same way with another processing. Let’s suppose for example a filter processing.

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In this way the user can obtain a chain of processing by dragging in the “Insert” node the desired element
from the list. The “Signals Quality” processing has been obtained in this way and added to the default
processing folder.

Manage panel: The below part of the page can be used to conclude the merge of the processing. By
inserting the title and the category of the new processing when the user clicks the Merge Processing
button the software will get all the processing in each node and in the insertion order of the graph and it
will create a new processing folder that will be filled with all the step folders found inside the involved
processing.

Node details panel: There is one last page section that need to be discussed and that is initially hidden
in the software. Each node can be opened and expanded to visualize what are the steps inside of it, to
do it the user can just move over the desired node until the writing “Expand” is visible. If the user clicks
with mouse on it, this will open a new panel near the graph editor which contains all the steps inside that
processing and the node title will be substituted with the “Expanded” writing. This means that the graph
editor can be used to explore the content of a processing, let’s assume that we have a merged processing,
and we want to see its steps without opening the proper folder, the user can just drag it in the insert
node, click on it and check the Node details panel. Let’s see an example with the Signals Quality
processing.

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The right panel will contain all the steps included in the expanded processing node under the shape of a
graph. Each step will have its own description and will be executed in the exact same order of the graph.
So, if the user creates a merged processing with a lot of steps, to check them in a graphical visualization
he can move the merged processing just created in the “Insert” node and expand it as explained before.

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Trigger Sampling
The purpose of this feature is to refresh a particular channel, visualized in a separate window, every
time a stimulation occurred. In order to access this feature the user should navigate to the realtime
window, start an acquisition (check related chapter of the manual) and click on the Trigger Sampling
button.

The first window that appears is the configuration window that allows to setup all of the parameters
needed by the Trigger Sampling mode.

In details:

1) Trigger track: the list is filled only with single tracks (AUX channel for example). The selected
track is used to refresh the evoked response plot when the threshold is reached.
2) EMG track: the list is filled with EMG track (grids, matrices, arrays, bipolar). Select the track you
want to take the data from.
3) EMG channel: select the channel of the grid you want to see in the evoked response plot.

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4) Trigger threshold: value used to refresh the plot. This value is expressed in the same unit of
measurement of the Trigger track. So if it's in volt, write the value in Volt.
5) Length of popup window: specify the plot x-axis time. This value is used to bufferize the data,
consider that data comes from device every 0.0625 second and contains fsamp/16 samples
circa.
6) Vertical cursors: insert vertical lines where to create areas and calculate the Peak-to-peak.

Once the user have decided each parameter and clicked “OK!”, the software opens the Trigger
Sampling window.

The screenshot was taken without a real setup and the signal display a channel with no sensor
attached. There is no useful information about the EMG channel but it’s good enough to describe the
window and its parts.

The top part contains a plot of the data with the same time visualization specified in the setting window
(length of popup window). Vertical scale instead is automatically adapted based on the data.

When the Trigger Track exceed the threshold, the data of the selected EMG track are displayed in this
new window and a new record is added in the table.
The plot contains four different vertical bars (two blue and two red ones), that are used to determine
two separate areas. Using the mouse is possible to select and more each separate line. This areas are
use to calculate the peak-to-peak value of the data and place this information in a table record.

The table colums are:

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1) STIM ID: stimulation ID used to identify the record of the table

2) 1-2 (mV): peak to peak value of the data inside blue zone
3) 3-4 (mV): peak to peak value of the data inside red zone
4) Cursor 1 (ms): time position of cursor 1
5) Cursor 2 (ms): time position of cursor 2
6) Cursor 3 (ms): time position of cursor 3
7) Cursor 4 (ms): time position of cursor 4

In the top right part there are three buttons:

1) Save button: can be used to save the plot as a picture

2) Left/right arrows: can be used to navigate the table and visualize old plots.

Navigation between old plots is also possible by selecting a record of the table with the
mouse left click.

One last button can be used to export the table as a csv file.

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Matrix Creator
The Matrix Creator tool is a feature designed for users who need to create custom matrices for
signal acquisition. These matrices, composed of rows and columns of electrodes, can be
tailored with varying shapes, sizes, and configurations, enabling precise customization for
different applications.

To access the Matrix Creator, navigate through the main menu and enter the setup section of
the software. From there, select the Matrix Creator button.

This action opens a new window where the tool is displayed, with a default matrix at the
center of the screen. The interface is intuitive, offering a variety of options to modify and
customize the matrix according to the user’s needs.

Surrounding the default matrix are buttons marked with + and - symbols on each side. These
controls allow users to increase or decrease the number of rows and columns in the matrix. As
the matrix is adjusted, users can further refine the design by adding or removing individual
channels. This is done simply by clicking on specific cells within the matrix.

By clicking the rotate button, users can view the backside of the matrix, where they can
manually assign channel indices to each electrode. This manual assignment provides an extra
layer of control, allowing for meticulous configuration of the matrix. However, for users who

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prefer automation, there is also a button that automatically assigns channel indices,
streamlining the process and ensuring consistent channel numbering.

Beyond configuring the shape and channel assignment, the Matrix Creator offers additional
customization options. Users can adjust the size of the electrodes and the intraelectrodic
distance (IED), which is the spacing between electrodes. Once all adjustments are made, users
can assign a unique name to the matrix, making it easy to identify and manage among multiple
configurations.

On the left side of the Matrix Creator window, there is a list of previously saved matrices, each
represented as a button. By clicking on one of these buttons, the corresponding matrix is
loaded into the main editor window, allowing for quick access and further modifications if
needed. This feature is particularly useful for users managing multiple matrices, as it simplifies
the process of organizing, retrieving, and modifying existing configurations.

Once the matrix is fully customized and saved, it can be seamlessly integrated into the setup
tool. The Matrix Creator is designed to work with the setup tool, ensuring that the custom
matrices are accurately reflected in the device configuration.

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Signal Processing
OTBioLab24 allows to process any kind of signals managed by the software itself. The processing tools
are available in the offline window and all the processing are accessible under the Processing menu.
There are processing plugins that can be only applied to single tracks and other processing can be applied
both to a single track or to a grouped track. Each processing can run on a selected range using the manual
selection or can be applied to the entire selected track.
All the processing tools do not change the recorded signals but generate new tracks under the last
existing track.

Absolute value
The plugin, when applied, simply rectify the signals.
Practically, it returns a new non-negative signal without regarding to its sign:
𝐴𝑏𝑠_𝑣𝑎𝑙𝑢e = |𝑠(𝑡)|
Where s(t) is the original signal.

Average Rectified Value - ARV

The estimation of ARV (AARV) is obtained for the epoch i using the following formula:
𝑁
1000
𝐴𝐴𝑅𝑣 (ⅈ) = ∑|𝑥𝑘 |[𝜇𝑣]
𝑁
𝑘=1

where:
‘N’ is the number of samples per epoch
‘xk’ is the amplitude of the signal at the input of the amplifier in mV.
‘1000’ allows to obtain the result in μV.

Epoch Average
The estimation of Epoch Average is the mean value of each epoch. Graphically, it is represented by a
point for each epoch.

Mean Square
The estimation of Mean Square is obtained using the following formula:
𝑁
1
Mean Square = ∑ 𝑥𝑘2 [𝑚𝑣]
𝑁
𝑘=1

where:

‘N’ is the number of samples

‘xk’ is the amplitude of the signal at the input of the amplifier in mV.

Max Min Mean

This processing computes max, min, mean and peak to peak value of the selected signal, and displays a
window in which these values are. Also, you can click on “Set as scale” and the min and max value are
set as track vertical range.

In particular it works comparing all the subsequent points of the selected track (memorized in a vector),
finding the maximum or the minimum one. The mean is simply obtained as follow:

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∑𝑛𝑖=1 𝑥𝑖
𝑚𝑒𝑎𝑛 =
𝑙𝑒𝑛𝑔𝑡ℎ
Where n is the number of elements in the vector.

Root Mean Square - RMS

The estimation of RMS (ARMS) is obtained for the epoch i using the following formula:

𝑁
1
𝐴𝑅𝑀𝑆 (ⅈ) = 1000√ ∑ 𝑥𝑘2 [µ𝑉]
𝑁
𝑘=1

where:

 ‘N’ is the number of samples per epoch.

 ‘xk’ is the amplitude of the signal at the input of the amplifier in mV.
 ‘1000’ allow to obtain the result in μV.

Signal-Noise Ratio - SNR

The estimation of Signal to Noise Ratio is computed as the Ratio between the highest RMS value of the
track and the lowest one.

Filtering
This processing tool can be applied both to single tracks and multiple tracks. When running it, a request
of filter type and corner frequencies is displayed. It is possible to choose between different type of
filters, whose expressions are represented below:

Low pass

𝐾𝜔02
𝐻(𝑠) = 𝜔
𝑠 2 + ( 𝑄0 ) 𝑠 + 𝜔02

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Band pass
𝜔
𝐾 ( 𝑄0 ) 𝑠
𝐻(𝑠) = 𝜔
𝑠 2 + ( 𝑄0 ) 𝑠 + 𝜔02

High pass

𝐾𝑠 2
𝐻(𝑠) = 𝜔
𝑠 2 + ( 𝑄0 ) 𝑠 + 𝜔02

Stop band

𝐾(𝑠 2 + 𝜔02 )
𝐻(𝑠) = 𝜔
𝑠 2 + ( 𝑄0 ) 𝑠 + 𝜔02

Moreover, the corner frequencies are differently asked depending on the filter type selected. The signals
generated by the filtering process are added as single or multiple tracks in the review window leaving
unaltered the starting signals. All filter types are II order Butterworth filters.

Median Frequency - MDF

The estimation of MDF (fMDF) is obtained by comparing the total signal spectrum intensity divided by
two with the cumulative intensity (i.e. all the intensity values for frequencies lower and including the
focal intensity). The lowest frequency retrieving the cumulative intensity bigger than the half total
intensity is fMDF.

Mean Frequency - MNF

The estimation of MNF (fMNF) is obtained for the epoch i using the following formula:
∑𝑛𝑘=0 𝐼𝑘 ⋅ 𝑓𝑘
𝑓𝑀𝑁𝐹 (ⅈ) = [𝐻𝑧]
∑𝑛𝑘=0 𝐼𝑘

where:

‘n’ is the number of frequency bins in the spectrum

‘fk’ is the frequency of spectrum at bin k of n
‘Ik’ is the Intensity of spectrum at bin k of n

Fast Fourier Transform - FFT

The FFT can be estimated from single tracks on the desired number of epochs. After selecting the track,
a window will appear for selecting the number of samples that will be used to obtain an averaged FFT to
reduce the noise in the estimated power spectrum. A minimum of 256 samples for the averaged FFT is
required. The maximum number of samples is equal to the length of the data. From this menu the user
can select the window functions to apply to the time domain data for estimating the FFT (rectangular,
hanning, hamming, blackman). Samples used to obtain the averaged FFT can be overlapped (50 % of
overlap - Welch’s method) or no overlapped (Barlett’s method) selecting the options that appears on the
bottom-right of the window menu.

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After selecting these options, a new window will display the result of the algorithm. Details about the FFT
algorithm can be found at http://sourceforge.net/projects/kissfft.

After the FFT has been estimated, keeping the left mouse button pressed
a rectangular window can be drawn to indicate the area that the user
wants to zoom in. When a right click on the FFT zoom out will be
performed.

Power Spectral Density - PSD

The power spectral density (PSD) can be estimated from single or multiple tracks on the desired number
of epochs. As in the FFT plugin, after the selection of the track, a window will appear in which you can
choose the window type (rectangular, hanning, hamming and blackmann) and the number of samples,
from a minimum of 256, that will be used to obtain an averaged FFT to reduce the noise (see FFT plugin
for details), the window functions and the method (Welch or Bartlett’s method).

After selecting options of this menu two plots will show the PSD of the signal in two different units: dB/Hz
and mV2/Hz. As an example, a PSD signal is shown in logarithmic scale.

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Average
The Average i calculated as:
𝑛
1
𝐴𝑣 = ∑ 𝑥𝑖
𝑙𝑒𝑛𝑔ℎ𝑡(𝑥[ⅈ])
𝑖=1

Where:
xi is a component of the vector x[i] of n elements (in fact the operation is integrated in a for cycle)

Coefficient of Variation - CoV

The coefficient of variation is calculated as:
𝜎
𝐶𝑉 = ∙ 100
𝜇
Where:
σ is the standard deviation
μ is the mean

Binarization
The processing Create Binary Track allows you to set a threshold: all the values above this threshold will
be set to 1, the remaining value (which are value lesser than the threshold) are set to zero, or vice versa,
depending on the ThresholdParameters you choose.

It could be useful for highlighting interesting parts of the signal or

eliminating minor parts of the signal.

Linearization and Parabolic

The linear and parabolic approximations are two methods that use an affine function to approximate the
original signal in a simplified way. They are used in the finite difference method for solving complicate
equation, also in this case of EMG signal acquisition.

Standard Deviation
The Standard Deviation is calculated as:

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∑|𝑥 − 𝜇|2
𝑆𝐷 = √
𝑁

Where
X is a generic element of the vector
μ is the mean
N it the length of the vector

It’s a statistic measure of the amount of variation or dispersion of all the vector’s values resulting from
the acquisition.

Band Pass EEG

This processing will extract from each signal (each channel) the
characteristic 5 bands of the EEG signals. Each of them has a specific
frequency range, as you can see in the figure on the right, and it’s related
to a different functional-brain status.

In particular, the alfa band it’s the oscillatory component ad it’s the ruling
frequency in the human EEG. Its power spectrum is represented by the
following formula:

Calibration
This processing is used to multiply the data for a specific value and to remove the offset. Both these
choices are optional, and the user can select one or both.

Convolution
This processing performs convolution between two signals in order to recognize the highest cross
correlation between them and how the shape of one is modified by the other. Once it recognizes it, it
will shift in time the second signal in order to align them.

Where:
f(t) is the first signal
g(t) is the second signal
τ is a generic time constant

For doing this process it is necessary to select two tracks because of the convolution’s definition,
otherwise it will not work.

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Derivative
Performs derivative of a signal. The first derivative of a signal is the rate of change of amplitude with the
time, which is interpreted as the slope of the tangent to the signal at each point.

Envelope
Extract the envelope from a single track and normalize it with respect to the envelope maximum peak.
The tool has been designed for EMG signals, the resulting signal is obtained by rectifying the desired signal
and applying a II order Butterworth low pass filter with 5 Hz corner frequency to the rectified signal.

The frequency response of the II order Butterworth filter is defined as follows:

1
|𝐺(𝜔)| =
√1 + 𝜔 2𝑛
Where:
𝜔 is the angular frequency
𝑛 is the order, in this case n=2

Instead, the first order low-pass filter eliminates everything under the frequency of 5Hz, whose Laplace
transform is:
𝜔0
𝐻(𝑠) =
(𝑠 + 𝜔0 )

Integral
Performs the integral of a signal which is the continuous analog of a sum. A definite integral of a function
can be represented as the signed area of the region bounded by its graph and the horizontal axis.

Sum
This processing tool can be applied to a multiple track or to, at least, a pair of single tracks. Simply it
calculates, sample by sample, the sum between signals. When it is applied to a multiple track, it calculates
the sum between all channels associated to the selected sensor and retrieve a new single track containing
the sum. A typical application is the use with signals from an electrode array; the processing calculates
the signals virtually obtained with multiple inter-electrodic distance.

Activate Instant Detection - AID

This processing tool estimates the muscle on–off timing, based on a physical model of muscle activation
rather than on a phenomenological one. Muscle activity is recognized based on the presence of MUAPs
in the surface EMG signal.

The surface EMG signal is the sum of the MUAP trains. A basic function can be assumed to roughly
describe the shape of a generic MUAP detected on the skin surface and the train is indicated with
MUAPT(t).

The EMG signal s(t) can therefore be expressed as:

𝒕−𝜽𝒊𝒋
𝒔(𝒕) = ∑𝒋 𝑴 𝑼𝑨𝑷𝑻𝒋 (𝒕) + 𝒏(𝒕) = ∑𝒋 ∑𝒊 𝒌𝒋 ⋅ 𝒇 ( 𝜶𝒋
) + 𝒏(𝒕) (1)

where:
j indicates specific MU
𝑘𝑗 is an amplitude factor

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𝜃𝑖𝑗 are the occurrence times of the MUAPs of the MU

𝛼𝑗 is the scaling factor
𝑛(𝑡) is the additive noise

In the case 𝜶𝒋 = 𝜶0 , ∀𝑗 and n(t) being white noise, one single event is repeating in the signal with a
known shape and unknown amplitudes and times of occurrence. In this case, the matched filter (CWT) is
the optimal filter for detecting the presence of a MUAP.

+∞
𝟏 𝒕−𝝉
𝑪𝑾𝑻(𝒂, 𝝉) = ∫ 𝒔(𝒕) ⋅ 𝒘∗( ) ⅆ𝒕 (2)
√𝒂 𝒂
−∞

where:
s(t) is the signal to be analyzed
w(t) is a prototype function (mother wavelet)
τ is a translation index
a is a scale parameter related to the frequency content

The CWT acts as a filter whose impulse response h(t) is equal to w(-t).

The event detection is applied to the filter (CWT) output and an amplitude threshold function 𝜂(t) is
defined as 𝜼(𝒕) = 𝐦𝐚𝐱{CWT(𝒂, 𝒕)}, based on the noise level.

The amplitude M of the maximum of the test function 𝜂(t) within the interval (0 < t < Tnoise), initial period
in which the EMG activity is not present, is used to set the threshold value as:

𝑴 = 𝒎𝒂𝒙{𝜼(𝒕)} (3)

𝒕𝒉 = 𝜶 ⋅ 𝑴 where 𝜶>1 (4)

The revealed vector is set at one for the time periods during which 𝜂(t) exceeds the threshold and zero,
otherwise. If the SNR is high, the choice of the value 𝜶 is not critical, due to the great amplitude difference
between EMG signal and noise. If the SNR is low, a low value of 𝜶 becomes a conservative choice.

After the detection process, events identified and separated by a temporal distance smaller than 125 ms
are considered as belonging to the same contraction and merged. This value (125 ms) corresponds to a
global muscular firing rate of eight pulses per second (pps), which is arbitrarily assumed as the lowest
effective muscle activity. After the merging of activity bursts closer than 125 ms, the detected events
shorter than 5 ms are attributed to either isolated MUAPs or noise related spikes and disregarded.

The algorithm is described in the paper: “A Fast and Reliable Technique for Muscle Activity Detection
From Surface EMG Signals. A.Merlo, D. Farina & R. Merletti, 2003, IEEE Transaction on Biomedical
Engineering, VOL. 50, NO. 3.”

When the Activation Instant Detection plug-in is selected, the window shown in figure 10.3 appears. The
Initial noise section and the Alpha value correspond to the initial interval and the alpha parameter of the
formulas (3) and (4). While the Minimum size of an inactivity should be greater than 125ms and the
Minimum size of an activity should be between 5 - 40ms.

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Find Zeroes
This plug-in produces a square waveform with a value equal to 1 where there are zeroes and a value
equal to 0 where it has found signal. To identify zero value, must find a zero and compare it with the next
10 samples if they are all zero then score. On the raw signal it is difficult to identify 10 samples equal to
zero while on the already processed signal it is more performing.

Normalization
The Normalization rescale all the values in a track given a specific max and min value.

𝑁𝑜𝑟𝑚(𝑥𝑖 ) = (𝑥𝑖− 𝑥max ) / (𝑥𝑚𝑎𝑥 − 𝑥𝑚𝑖𝑛 )

Where:
xi is a component of the vector x[i] of n elements (in fact the operation is integrated in a for cycle)

Time Shift
This processing will shift the signal in time, and it is applicable only on a single track. When you run this
processing, it will ask you how many samples you want to shift the signal. If the number is negative, it
will move the beginning of the signal forward in time, delaying it. If it will be positive, it will remove the
first part of the signal.

Decomposition (coming soon)

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EEG Impedance Check

The EEG impedance check is a feature used to shows the electrode-skin impedance and let the user
understand if the electrode contact is good enough to allow reliable recording. On the headset diagram
the different electrodes positioned on the head are represented by a circle. For each one the electrode-
skin impedance value is calculated using the "Lead-Off Detection" function present in the
sessantaquattro and sessantaquattro+ ADC converter and a color code is associated to this value which
varies between red (not good) and green (low impedance).

Red: greater than 80 kohm

Orange: 25-80 kohm

Green: less than 25 kohm

This feature can be used from the setup window, after selecting any device that allows to use it, an orange
button appears.

When it’s clicked a new window appears and the visualization can be different depending on the adapter
and sensor inserted.

1) Default visualization: show the pin out of the device itself and the impedance value for each
channel.

2) EEG Cap visualization: show the impedance in a graphical representation of the EEG cap, based
on the number of channels of the cap itself.

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Troubleshooting

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