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NeuroScope2 Menu Bar

Here is a detailed description of each of the menu elements of NeuroScope2.

  1. NeuroScope2
  2. File
  3. Session
  4. Cell metrics
  5. BuzLabDB
  6. View
  7. Settings
  8. Help

NeuroScope2

ElementsDescription
About NeuroScope2Shows dialog with basic info about NeuroScope2
QuitQuit NeuroScope2. This will save automatically save the session metadata. Closing the main window has the same effect.

File

ElementsDescription
Load session from folderOpens a file dialog where you can select a folder to load
Load session from fileOpens a file dialog where you can select a file to load
Recent sessions…Shows a list of recently active sessions.
Export to .png file (image)Exports screenshot to .png file as image graphics
Export to .pdf file (vector graphics)Exports screenshot to .pdf file as vector graphics
Export figure via the export setup dialogExport figure via the export setup dialog

Session

ElementsDescription
View metadataShows the session GUI (session metadata)
Save metadataSave the session metadata
Open basepathOpens the basepath of the current active session in finder/explorer

Cell metrics

ElementsDescription
Open group data dialogOpens the group data dialog
Save cell_metricsSave cell metrics

BuzLabDB

This menu is for lab members that has credentials to the Buzsaki lab databank at https://buzsakilab.com/wp/database/. Please see this CellExplorer database page for further info.

ElementsDescription
Load session(s) from BuzLabDBShows the database dialog with list of sessions with calculated cell metrics.
Edit credentialsOpen the database credentials file db_credentials.m, where you can define your Buzsaki lab databank credentials
Edit repository pathsOpen the database credentials file db_local_repositories.m, where you can define the local paths to data repositories used by CellExplorer and the database tools
View current session on websiteShows the current session in the Buzsaki lab databank in your browser
View current animal subject on websiteShows the current animal subject in the Buzsaki lab databank in your browser

View

ElementsDescription
Summary figureGenerates a summary figure containing the full timeline of external data currently active in NeuroScope2, e.g. spikes, events, states, behavior and trials, time series
RMS noise across channelsGenerates a figure with RMS across electrodes
Power spectral density across channelsGenerates a power spectral density plot for all active channels
Power spectral density across channels (log bins; slower)Generates a power spectral density plot, with log bins, for all active channels. Slower but more informative

Settings

ElementsDescription
Show full menuboolean Hides the NeuroScope2 menu and shows the regular Matlab figure menu bar. Press M to reverse.
Remove DC from signalboolean Substracts the mean of each trace (DC-level)
Show channel numbersboolean Shows channel numbser left of the traces
Show scale barboolean Shows a scale bar in the upper left corner of the traces
Narrow ephys paddingboolean Decreases the vertical padding above and below the ephys traces
Dynamic ephys range plotboolean Alterns how the “range” plot style acts. In dynamic mode, the range style will only be applied for windows sizes larger 1.2s, otherwise all samples will be plotted. Matlab performs well up to a upper limit of simultaneously plotted samples (~1 second at 20KHz, 128 channels), after which it becomes significantly faster to plot a subset of the points.
Color ephys traces by channel orderApply the colormap by channel order instead of by electrode groups. Select the number of color groups (1-50)
Change colormap of ephys tracesChange the colormap applied to the ephys traces (default to the electrode groups).
Change colormap of spikesChange the colormap applied to the spike rasters.
Change background color & primary color (ticks, text and rasters)Changes the color of the trace background (black) and the primary color (white; ticks, text, and rasters)
Show detected events below tracesboolean Shows detected events below traces.
Show detected spikes below tracesboolean Shows detected spike raster below traces.
DebugToggle debug mode

Help

ElementsDescription
Mouse and keyboard shortcutsShows a window with the list of mouse and keyboard shortcuts
CellExplorer websiteOpen the CellExplorer website in your browser
About NeuroScope2Open the NeuroScope2 page from the CellExplorer website in your browser
Tutorial on metadataOpen the Session metadata tutorial from the CellExplorer website in your browser
Documentation on session metadataOpen the session metadata documentation page from the CellExplorer website in your browser
SupportOpens the CellExplorer website describing support options
Submit feature requestSubmit a feature through the CellExplorer GitHub issue system
Report an issueReport an issue through the CellExplorer GitHub issue system