NESO

NEural SOrter
NESO

Daniel de Santos Sierra-Cristina Soto Sánchez

UNED-GB2S
UMH-CIBER-BBN

Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN

NEural SOrter

NEural SOrter
NESO

NEural SOrter or NESO is a powerful,
easy-to-use free software tool for oine
electrophysiological recording analysis.
NESO has been developed by Daniel de
Santos Sierra and supervised by Dr Cristina
Soto Sánchez at the UMH Bioingeneering
Institute directed by Dr. Eduardo
Fernández Jover.
https://sourceforge.
To download it:
net/projects/neuralsorter/
Contact emails:
B desantossierra@gmail.com
B dsantos@cedint.upm.es


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What can I do with NESO? (I)

NESO is a work in progress whose developer is adding features continuosly.
NESO oers new exclusive features like:
supports linux
analyzes many les at once
classies as the same unit the same waveforms cointained in separated
les at once
spike viewer allows you to select and delete artefacts very easily just
dragging the cursor
selects spikes manually to sort or delete them with just one click


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What can I do with NESO? (II)

At this point you can:
analyze NeuroShare and MultiChannel Systems recordings
view your recordings as superimposed waveforms or as waveforms in
time
use Principal Component or Height vs Width analysis to extract
waveform features
use Vectorial Quantization or K-Means anaysis to sort the
waveforms (spikes)
classify spikes as diferent units
use templates to sort spikes
save the analysis results as NeuroShare format


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NESO

NEural SOrter - NESO

Free software under GPLv3
Developed in C++ with Qt4 and
Qwt frameworks
Operative Systems: Windows, Linux
and Mac OS X
Computer architecture: 32-bits or
64-bits
Memory minimum requirements: at
least double of the *.nev le size to
be opened


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GUI
Divisions

NESO GUI consists of four areas:
1 Toolbar: File, Electrodes, Methods,
Templates, View, Window, ?
2 Workspace: area where NESO
windows are shown
3 Progress Bar shows the degree of task
completion
4 Information: shows process
information. It hides by clicking on
the left button


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Toolbar (I)

NESO recognizes MCS les in TXT format and NEV les
Open File: to open a new data le: *.nev or *.txt

Save File: to save the analyzed data in a NEV format

Close All Files: It closes all opened les

Click to select the channels to analyze
Methods to extract features and analyze waves
We can use Templates tab to
Load saved templates
Save created templates in a le
Create templates from all units and all the electrodes


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Toolbar (II)

NESO shows data as
- waveforms vs time, Raw View
- superimposed waveforms aligned at the threshold crossing
times, Spike View
We can open as many windows (Raw or Spike) as we want
but we have to take in account that each window viewer
requires RAM consumption
To tidy up our workspace, we can use Cascade or Tile to
order all opened windows
We can see the interactive help by clicking on Help
About tab shows NESO information


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File Formats

Readable formats:

Neuroshare les (*.nev)

MultiChannel Systems in TXT les (*.txt)
1

Template les (*.tem)

Saved les:

Neuroshare les (*.nev)

Template les (*.tem)

1
Use MC_DataTool to export *.mcd spikes to *.txt

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File Menu
Open File

To open a le:

1 click on File Open File
2 select a le with a readable format ( *.nev or *.txt, not *.tem)
3 click Open to open a selected le or cancel to exit
When a le is opened you will see a conrmation message in blue in
the information area. If a le can not be opened or if you cancel
the selection, Unknow format message is shown in red.


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File Menu
Save File

To save data as *.nev le:

1 click onFile Save File
2 type the le name

3 click Save to save the data into the current le or click cancel
to exit without saving

Save File, saves as many les as you have opened and keeps them
opened.


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File Menu
Close All Files

To close opened les and to restore NESO to the initial state click
on File Close All Files. The next window automatically shows
up

Click on:

Save to save les and then close them

Discard to close les without saving (the data changes will be
lost)

Cancel to keep the le opened


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Electrode Selection

Once we open a le, we have to select the electrodes we want to
analyze. To do that, click on Electrodes Selection.
The left panel shows the electrodes to analyze and the right panel
the ones to reject.
All Deselects all the electrodes.

Deselects all the highlighted

electrodes.

Selects all the highlighted

electrodes.

All Moves all the electrodes to

the left panel.


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Spike Sorting (I)

Once we selected the electrodes (Slide 13) we can do spike sorting.
Spike sorting splits the dierent waveforms contained in a
recording. We call unit to all spikes red by a single neuron.


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Spike Sorting (II) Options

1 allows you to select all the opened les or just
Files

one of them (to do spike sorting analysis).
Electrode allows you to select all or just one of the

electrodes from the previous selected les.
Unit allows you to select all the units of the selected
electrodes.
2 Selects the time window where you want to extract
features from
3 Menus to extract waveforms features and perform
sorting. (Slide 16)
4 Quick Calculate extracts features and performs spike
sorting in one step using default values. Sort ALL
with templates do spike sorting with saved

templates.


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Spike Sorting (III)
Options: Features Sorting

Select one method Select Vectorial Quantization or K-Means
and click Calculate to to sort features into units. If all electrodes
extract features from are selected then a default number of
waveforms.
features are selected to sort them. You can
Methods: Principal
select the extracted features you want to
Component Analysis
use manually. Remember that to sort
and Height vs Width
features, you have to calculate them rst.
(Slide 17)


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Spike Sorting (IV)
Options: Features

Eleven features are extracted with Height-Width method.

Positive height (voltage
100
25
and time)
50 50
75 Negative height
Voltage [μV]

0
75
(voltage and time)
-50

-100
50 Peak-to-peak (time)
-150
25
Positive and negative
-200 peak widths at a given
0.000 0.333 0.667 1.000 1.333 1.667
Time [ms] height (25%, 50% y
75%)


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Spike Sorting (V)
Options: Sorting

To do spike sorting you have to extract features rst, then choose a
sorting method (Vectorial Quantization or K-Means, and click
Calculate).
Modify Threshold and K clusters to obtain more or less units.
If ALL electrodes is selected then NESO chooses default parameters
to do spike sorting. If one electrode is selected then you can tick
Please, choose parameters by default to use default
parameters, or you can choose them manually.
See Slide 19 about for default and non-default parameters
information.


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Spike Sorting (VI)
Options: Sorting

Default parameters depend on the method used to extract features.
For PCA takes the rst three PCAs.
For Height-Width takes: Positive Height, Negative Height and
Peak-to-peak.
The non-default parameters are choosen with the following dialog
where the left column corresponds to parameters to use and the
right column corresponds to discarded parameters.


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Spike Sorting (VII)
Plot

Spike sorting plots extract features as colored
points (color represent unit).
Electrode shows electrodes with features.
X-Axis and Y-Axis: features names

If dotted is checked features are shown as dots,
otherwise as a line joining the dots.


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Raw View (I)
Windows Regions (I)

1 2

3 5
6

7

4


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Raw View (I)
Windows Regions (II)

1 File and Electrode selection: Select one le or ALLFILES and
one electrode

2 Click on + to add that electrode to the plot

3 Vertical Scale: If only one electrode is added then the scale bar
is shown in Voltage. Adding more than one electrode the scale
bar shows the electrode name.

4 Horizontal Scale: time

5 Options: click on to show the options and to hide them.

6 When you add more than one electrode you can show the scale
as a oating legend

7 Spike data events in time


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Raw View (II)

Analog Mask: to show recorded trigger signal. There are 8
possible trigger channels.
Electrodes click Add All to add all electrode to the plot.
click Del All to clean the plot.
Legend scale Show Scale to show a oating scale in the plot.

Voltage scale in nV, µV, mV or V
Time scale in ms, s or min
to update scale values
to move the scale clicking on the plot
Pointer options: select to use normal pointer
select, drag and drop on the plot to
zoom in time or click to zoom out.
select, drag and drop to move the plot
in time


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Spike View (I)
Windows Regions (I)

1
2.1
2.2

2 3

2.3


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Spike View (I)
Windows Regions (II)

1 To show the spikes, select one le or ALLFILES, one electrode
and one or ALL units

2 Plot spike data. Dierent colors mean dierent units.

2.1 E:XX-U:YY(ZZ) where
E = electrode
XX = electrode number
U = unit
YY = unit number
ZZ = number of spikes
2.2 Voltage scale
2.3 Time scale in milliseconds

3 Click on to show the options and to hide them.


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Spike View (II)

Convert to: by clicking OK it converts spike Units shown in the
spike viewer (Slide 24-1) to the unit you select on this eld
Template options: see Slide 27
Pointer options select to use normal pointer
zoom in time or click to zoom out.
select spikes manually.
Tick on Grid to show a grid on the plot
Click on Rename units to change units identier
If Unit NOISE is selected, click Delete to remove spikes in this
unit permanently. If Unit is not NOISE then converts Unit into
NOISE.

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Templates (I)

A template is a wave that represents a set of spikes. We use mean
and standard deviation of these spikes to create new templates.
With NESO you can create one template from the spikes in one
unit. In the next gure, we can see spike data (dark blue) and their
template (cyan) where the solid line represents the data mean at a
given time and the dotted lines represent the standard deviation
(mean ±std).
E:27-U:3(125)
100

50
Voltage [μV]

0

-50

-100

-150

-200
0.000 0.333 0.667 1.000 1.333 1.667
Time [ms]


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Templates (II) - Spike View

Create Creates a template with all the spikes in one
template unit. If ALL units are selected then it creates as
many template as number of units
Delete To delete a template, select one template from
template the template list and click on Delete template.
Template List List of available templates in this electrode.
Split with... Separates spikes that t better with one template and creates a
new unit with them. Spikes that don't t with either template
remain as the same unit.
Resort with... Classify all the spikes as the template which ts better. As a
result, we have as many units as number of templates.
Show... Check this box and select one template from the template list
to show it on the plot.

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Templates (II) - Sorting Options

Sorting Options window shows a button to Sort ALL with
templates that classies all the spikes in each electrode with loaded
or calculated templates in that electrode. If there are not templates
in one electrode then the spikes of that electrode won't be sorted.


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Templates (II) - Toolbar

With the toolbar, we can:
Open a template le Open template
Save templates in a le Templates Save Templates
Create templates from all electrodes All Units to Templates


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Acknowledgement

This project was supported by:
- Cátedra Bidóns Egara
- ONCE


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