NEural SOrter or NESO is a powerful, easy-to-use free software tool for offline electrophysiological recording analysis.
To download it: https://sourceforge.net/projects/neuralsorter/
NESO is a work in progress whose developer is adding features continuosly.
NESO offers new exclusive features like:
- supports linux
- analyzes many les at once
- classifies as the same unit the same
- waveforms cointained in separated files 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
At this point you can:
- analyze NeuroShare and MultiChannel Systems recordings
- view your recordings as superimposed waveforms or as waveforms in time
- use PCA and 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
Developers:
Daniel de Santos Sierra
Cristina Soto Sanchez
1. 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
2. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
3. NEural SOrter
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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
4. NEural SOrter
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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
5. NEural SOrter
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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
6. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
7. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
8. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
9. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
10. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
11. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
12. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
13. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
14. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
15. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
16. 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)
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
17. 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%)
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
18. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
19. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
20. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
21. Raw View (I)
Windows Regions (I)
1 2
3 5
6
7
4
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
22. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
23. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
24. Spike View (I)
Windows Regions (I)
1
2.1
2.2
2 3
2.3
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
25. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
26. 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
select, drag and drop on the plot to
zoom in time or click to zoom out.
select, drag and drop on the plot to
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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
27. 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]
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
28. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
29. 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.
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
30. 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
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter
31. Acknowledgement
This project was supported by:
- Cátedra Bidóns Egara
- ONCE
Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBN
NEural SOrter