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CellExplorer Menu Bar

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

  1. CellExplorer
  2. File
  3. Navigation
  4. Cell Selection
  5. Classification
  6. Waveforms
  7. View
  8. ACG
  9. MonoSyn
  10. Reference data
  11. Ground truth
  12. Group data
  13. Table data
  14. Spikes
  15. Session
  16. BuzLabDB
  17. Help

CellExplorer

ElementsDescription
About CellExplorerShows dialog with basic info about CellExplorer
Edit preferencesOpens CellExplorer preferences, which are stored in preferences_CellExplorer.m
Run BenchmarksRun various benchmarks as showed in Supplementary figure 5
QuitQuit CellExplorer. This will save any manual curation to the output from the call, e.g. cell_metrics = CellExplorer('metrics',cell_metrics);. Closing the main window has the same effect.

File

ElementsDescription
Load session from fileOpens a file dialog where you can select a cell metrics Matlab file to load
Save classificationSaves any manual curation to the original cell metrics files. This also works in batch mode, allowing you to save any changes back to the original cell metrics calculated per session.
Restore classification from backupShows a dialog with a list of backup steps for the current session. Choose any backup point to restore to that state. Every time the cell metrics are processed again with ProcessCellMetrics.m and curation are saved via CellExplorer, a backup is created. Backups are stored in a subfolder with the data
Reload cell metricsReload cell metrics from original files
Export main figure windowExports the CellExplorer interface
Generate supplementary figureGenerates a supplementary figure optimized for publication (see figures below with the dialog and supplementary figure). You can select which metrics to show in panels in C and D
Generate summary figureGenerates a summary figure, which is also generate by the processing module

ElementsDescription
Go to cellShows a dialog allowing you to provide a cell id or session to go to
Go to previously selected cell (backspace)Go to previously selected cell

Cell Selection

ElementsDescription
Polygon selection of cells from plotsDraw a polygon circling the points/lines in any of the plots to perform an action on the circled cells
Perform group actionPerform group action on selected cells. If no cells are currently selected, a selection dialog will be shown
Sticky cell selectionboolean: Cell the selection is kept: “sticky”
Reset sticky cell selectionResets cell selection
Highlight cells by mouse overboolean: whenever you move your cursor in any plot, a pop-up is shown for the nearest cell (relative to the cursor) in the plots with the cell’s id and group info (e.g. Cell type or other active grouping)

Classification

ElementsDescription
Undo classificationUndoes the last manual curation step (any curation of these types are tracked: cell-types, labels, tags, groups, brain regions, ground truth classification, Deep-Superficial)
Assign brain regionAssign/alter brain region of current cell
Assign labelAssign/alter label of current cell
Add new cell-typeCreate new cell-type
Add new tagCreate new group tag
Reclassify cellsReclassifies the cells using the standard classification from the Processing module
Agglomerative hierarchical cluster tree classificationAgglomerative hierarchical cluster tree classification. A dialog will be shown allowing you to select which metrics to include in the analysis
Adjust Deep-Superficial assignment for sessionOpens the Deep-Superficial GUI via gui_DeepSuperficial.m. Please see the Deep-Superficial tutorial for further info

Waveforms

ElementsDescription
Z-score waveformsboolean: Waveforms are z-scored or shown in µV in the Waveforms (all) plot
Show waveform metricsboolean: Show waveform metrics in the single waveform plots. Metrics include trough-to-peak, AB-ratio, trough-to-peak (derivative)
Channel map inset with waveformsNo channelmap/Single units/Trilateration of units: Shows a small channel map inset in the waveform plots
Show group colors in channel map insetboolean: Show group colors in channel map inset
Show ACG inset with waveformsboolean: Shows a small ACG inset in the waveform plot
Waveform alignmentProbe layout/Electrode groups
Waveform count across channelsAll channels/Best channels Shows waveforms for all or only for the best channels
Trilateration group datasession/animal/all show trilaterated position of units from current session, from the same animal or from all sessions (only in batchmode). Only affects the trilateration position plot and not the Channel map inset in the waveforms plot

View

ElementsDescription
Show regular Matlab menu barboolean Hides the CellExplorer menu and shows the regular Matlab figure menu bar
Show all tracesboolean All traces are shown instead of the default maximum of 2000 (on by default to increase performance)
Show legend in spikes plotboolean Shows legend in spikes plot (off by default to increase performance)
Show linear fit in group plotboolean Show a linear fit along thet 2D group data in the custom plot
Show legend in firing rate mapsboolean Show legend in firing rate maps (off by default to increase performance)
Show heatmap in firing rate mapsboolean Show heatmap of trials in firing rate maps (headmap or lines)
Shown colorbar in heatmaps in firing rate mapsboolean Show colorbar in heatmaps (off by default to increase performance)
ISI normalizationRate/Occurrence/Instantaneous rate Alter the normalization and x-axis of the ISI plots
Raincloud plot normalizationPeak/Probability/Count Alter the normalization of the raincloud histogram curves
Generate significance matrixDialog allowing you to select a list of metrics for which a significance matrix will be generated as described here
Generate raincloud metrics figureDialog allowing you to select a list of metrics for which a raincloud plot will be generated for each of them as described here
Change marker size for group plotsChange the marker size in group plots: size 6-25 recommended.
Change colormapDialog allowing you to change the colormap
Change metric used for sorting image dataDialog allowing you to change the metric used to sort cells in image data
Change metrics used for t-SNE plotDialog allowing you to change the metrics, parameters and recalculate the t-SNE data
Flip x and y axes in the custom plotFlips selected x and y metrics for the custom plot

ACG

ElementsDescription
ACG time scale30ms/100ms/1sec/Log10: adjusts the timescale of the ACG plots
Log y-axisboolean Logarithmic y-axis
Show ACG fitboolean Shows the ACG fit in the ACG plots

MonoSyn

ElementsDescription
Show in custom plotboolean Show monosynaptic connections in the custom plot
Show in classic plotboolean Show monosynaptic connections in the classic plot
Show in t-SNE plotboolean Show monosynaptic connections in the t-SNE plot
Plot excitatory connectionsboolean Show excitatory monosynaptic connections
Plot inhibitory connectionsboolean Show inhibitory monosynaptic connections
Synaptic filterNone/Selected/Upstream/Downstream/Up & Downstream /All: Which monosynaptic connection types to show.
Highlight excitatory cellsboolean Highlight excitatory cells with triangles
Highlight inhibitory cellsboolean Highlight inhibitory cells with squares
Highlight cells receiving excitatory inputboolean Highlight cells receiving excitation with downward facing triangles
Highlight cells receiving inhibitory inputboolean Highlight cells receiving inhibition with asterisks
Shown hollow gaussian in CCG plotsboolean Show the significance level for the monosynaptic connections in the CCG plots (determined from a hollow gaussian)
Adjust monosynaptic connectionsadjust monosynaptic connections for the current session using the gui_MonoSyn.m as described in the Monosynaptic connections tutorial

Reference data

ElementsDescription
Reference data plotting optionsNo reference truth data/Image data/Scatter data/Histogram data Options described here
Opens reference data dialogOpens the reference data dialog as described here and in this tutorial
Adjust bin count for reference and ground truth plotsAdjust the bin count (default: 100) for image and histogram representations
Explore reference dataReplaces current cell metrics data with the loaded reference data, allowing you to explore these cells natively in CellExplorer

Ground truth

ElementsDescription
Ground truth plotting optionsNo ground truth data/Image data/Scatter data/Histogram data Options described here
Opens ground truth data dialogOpens the ground truth dialog as described in this tutorial (dialog shown below)
Adjust bin count for reference and ground truth plotsAdjust the bin count (default: 100) for image and histogram representations
Show ground truth classification tabShows a tab with a list of ground truth cell-types in the right side-panel for manual curation (tagging). Please see this Opto-tagging tutorial to learn more
Save tagging to groundTruthData folderPlease see the Opto-tagging tutorial to learn more
Explore groundTruth dataReplaces current cell metrics data with the loaded ground truth data, allowing you to explore these cells natively in CellExplorer

Group data

ElementsDescription
Open group data dialogShows the group data window for groups/tags/groundTruthClassification. Group data can be selected, edited, highlighted, used as filters and actions can be performed from them.
Generate filters from group dataTakes group data (groups/tags/groundTruthClassification) and generates filters from them (check the drop-down in the left side panel in Group data and filters). Original group data can be overlapping, where a given cell can belong to many groups. If the filters generated, this is not preserved. Three new filter groups are created: groups_from_tags, groups_from_groups and groups_from_groundTruthClassification

Table data

ElementsDescription
Table data typeCell metrics/Cell list/None: Show cell metrics (full list of metrics and values) for current cell or list of cells (list of cells with a check box, id and two metrics for each cell) in table
Cell list metrics #1 and #2If cell list is shown in table, you can select what metrics to show in the list
Cell list sortingmultiple options The metric used to sort the cells in the table

Spikes

ElementsDescription
Open spike data dialogOpen the spike data dialog, also described in the tutorial on plotting spike raster data in CellExplorer

Session

ElementsDescription
View metadata for current sessionOpens the session metadata window using gui_session.m (shown below). Learn more about the session metadata
Open directory of current sessionShow the data directory of the current session in your file browser

Metadata interface

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

Help

ElementsDescription
Keyboard shortcutsShows a window with the list of keyboard shortcuts
CellExplorer websiteOpen the CellExplorer website in your browser
TutorialsOpen the tutorials page from the CellExplorer website in your browser