Menus¶

The menu bar, item by item. Shortcuts use macOS modifier names — see the conventions note.

File¶

Item	Shortcut	Does
Open Project	`Cmd`+`O`	Open the project dialog
New View	`Cmd`+`T`	Add a view to this window
New Window	`Shift`+`Cmd`+`N`	Open a second window
Close View	`Cmd`+`W`
Close Window	`Shift`+`Ctrl`+`W`
Open Recent ▸		Your recent projects, ending in Clear Menu

View¶

Item	Shortcut	Does
Command Palette…	`Cmd`+`Shift`+`P`	Search and run any command — see shortcuts
Connectivity Table	`Shift`+`Cmd`+`C`	Widget
Distance Heatmap	`Shift`+`Cmd`+`D`	Widget
Feature Comparison	`Shift`+`Cmd`+`F`	Widget
Meta Data Explorer	`Shift`+`Cmd`+`M`	Widget
Center ▸ Scatter		Reset the scatter view
Center ▸ 3D Viewer		Reset the viewer camera
Center ▸ Selection	`Shift`+`C`	Centre the scatter on the selection
Toggle Figure Controls		Show/hide the control panel (also `C`)
Toggle Viewer Controls		Show/hide the viewer sidebar
Reset Layout		Restore the default stacked 50/50 panes
Synchronize Viewer		Checkable, on by default. Couple scatter selection to the 3D viewer
Labels ▸ Show Labels	`L`	Checkable, on by default. Show/hide the point labels
Labels ▸ Declutter Labels		Checkable, on by default. Automatically arrange labels so they cover neither points nor each other
Labels ▸ Declutter Mode ▸		Individual Labels (default): every visible point gets its own label. One Label Per Group: a single label per unique value, with connector lines fanning out to all its points
Labels ▸ Connector Lines		Checkable, on by default. Draw a short line from each label to the point it belongs to
Labels ▸ When Labels Don't Fit ▸		What to do with labels that can't be placed without overlap: Hide (default), Show Dimmed (faded, drawn behind the points) or Show Normally
Show Hoverinfo		Checkable, on by default. Tooltips on hover
Hover Columns ▸		Which meta columns appear in the tooltip, plus Show All / Hide All

The four widget entries are disabled until a project is loaded. The Labels settings (except Show Labels itself) are remembered across sessions and apply to new tabs and windows.

Whether a widget can be opened depends on the data behind an embedding — a connectivity embedding may have features while a morphology one only has distances. So in a project with multiple embeddings, the first three entries become submenus and you pick the embedding to open the widget for:

View ▸ Feature Comparison ▸ connectivity (UMAP)
                            morphology (NBLAST) (no features)

Embeddings that lack the data are listed but disabled, saying what they lack; the entry itself is disabled only when none of them has it. Opening a widget this way does not switch the active embedding — the widget is titled with the embedding it belongs to, and each embedding gets its own. The keyboard shortcuts always open the widget for the active embedding.

Meta Data Explorer stays a single entry: meta data is shared by all embeddings of a project.

Selection¶

Item	Shortcut	Does
Select All	`Cmd`+`A` (macOS only)
Invert Selection	`Cmd`+`I`
Deselect All		Also `Esc` over the plot
Set Annotations	`Cmd`+`A` / `Ctrl`+`A`	Push annotations
Grow Selection	`Cmd`+`+`	Add nearest points
Shrink Selection	`Cmd`+`-`	Undo the last grow
Grow/Shrink Options ▸		Data source, feature metric, and how much to grow by
Find Nearest…		For each selected neuron, find its nearest neighbours from a filtered pool — see Find Nearest
Hide Selection	`H`
Show Hidden	`Alt`+`H`
Remove from View	`Backspace`	Selection views only
Open in New View	`Shift`+`Cmd`+`Ctrl`+`N`
Open in Neuroglancer		Open the selection in a Neuroglancer scene
Copy to Clipboard ▸ IDs	`Cmd`+`C`
Copy to Clipboard ▸ Meta Data

Select All and Set Annotations share Cmd+A on macOS

Not a conflict in practice — Select All is only bound on macOS, and Set Annotations uses Ctrl+A elsewhere. But it does mean the same chord does different things depending on your platform.

Grow/Shrink Options¶

Submenu	Contains
(data sources)	Exclusive group — which source the neighbourhood comes from
Feature Metric	Only when a feature source is active
Grow By	`N points` presets (points closest to the selection as a whole) plus a custom entry; `N nearest neighbours each` presets (each selected neuron pulls in its own nearest, so the two sides of the brain grow together) plus a custom entry; Within neighbour distance; and, in distance mode, a Distance × factor submenu

Export¶

Item	Produces
Meta Data ▸ To Clipboard	Tab-separated meta table
Meta Data ▸ To CSV	`<project>_meta_data.csv`
Embedding ▸ To Plotly	A self-contained interactive HTML page
Embedding ▸ To Dashboard	The same, with selection-linked panels
Project	A full project snapshot directory

See exporting your work.

Window¶

Item	Shortcut	Does
Zoom		Toggle maximise
Minimize	`Cmd`+`M`
Move View to New Window		Same as dragging a tab out vertically
Merge Window into Parent		Put a detached window's views back
Hide Widgets of Inactive Views		Checkable. Hide background views' widgets, restoring them with their view
Show Annotation Log		Every push this session
Show Project Details		The `info` file as a tree
Credentials...		Service tokens. On macOS this appears under BigClust → Preferences.

Help¶

Item	Does
Documentation	Open this site
About	Version and links. On macOS this appears under BigClust → About BigClust.
Check for Updates…	Query PyPI for a newer release
GitHub Repository	https://github.com/flyconnectome/bigclust2
Report a Problem	https://github.com/flyconnectome/bigclust2/issues
Debug ▸ Scatter / Viewer / All	Checkable, per view. Render debug overlays
Debug ▸ Labels…	Diagnose label placement for the current view: which labels were placed where, and why the rest were dropped (every rejected candidate position with its reason). Copy the report when reporting label issues
Debug ▸ Tracebacks	Checkable, app-wide. Include full tracebacks in the log
Keyboard Shortcuts	The list on this page

Debug → Tracebacks is what to turn on before reporting a problem.