NESO

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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

Published in: Health & Medicine, Technology
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NESO

  1. 1. NEural SOrter NESO Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  2. 2. NEural SOrterNESO 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.esDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  3. 3. NEural SOrterWhat 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 clickDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  4. 4. NEural SOrterWhat 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 formatDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  5. 5. NEural SOrterNESO 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 openedDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  6. 6. GUIDivisions 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 buttonDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  7. 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 electrodesDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  8. 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 informationDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  9. 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 *.txtDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  10. 10. File MenuOpen 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-BBNNEural SOrter
  11. 11. File MenuSave 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-BBNNEural SOrter
  12. 12. File MenuClose 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 openedDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  13. 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-BBNNEural SOrter
  14. 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-BBNNEural SOrter
  15. 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-BBNNEural SOrter
  16. 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-BBNNEural SOrter
  17. 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-BBNNEural SOrter
  18. 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-BBNNEural SOrter
  19. 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-BBNNEural SOrter
  20. 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-BBNNEural SOrter
  21. 21. Raw View (I)Windows Regions (I) 1 2 3 5 6 7 4Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  22. 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 timeDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  23. 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 timeDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  24. 24. Spike View (I)Windows Regions (I) 1 2.1 2.2 2 3 2.3Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  25. 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-BBNNEural SOrter
  26. 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-BBNNEural SOrter
  27. 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-BBNNEural SOrter
  28. 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 dont 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-BBNNEural SOrter
  29. 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 wont be sorted.Daniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  30. 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 TemplatesDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter
  31. 31. Acknowledgement This project was supported by: - Cátedra Bidóns Egara - ONCEDaniel de Santos Sierra-Cristina Soto Sánchez UNED-GB2S UMH-CIBER-BBNNEural SOrter

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