Figure

Compose publication figures from plots, images, text and 3D models.

6 min readFigures
The Figure workspace with a multi-panel neuroscience figure on the canvas, the Figures and Layers sidebar on the left and the Inspector on the right.
The Figure workspace keeps a multi-panel composition, its layers and its export controls together. Data and anatomy: Allen Institute for Brain Science and MICrONS. Visual credits.

The workspace

Shortcuts are written with Ctrl and Alt. On macOS, press ⌘ Command for Ctrl and ⌥ Option for Alt; Keyboard shortcuts lists every Figure shortcut.

Finding and naming figures

Open All… in the Figure sidebar, or Reference, sources & used in… in the Inspector, for the project-wide figure catalog. Search by title, designation, reference key, or canvas. Each result has a preview, source status, and links to the saved documents that use it. Paper’s insert and reference pickers show the same title, designation, canvas, and key.

A figure has three distinct labels:

Paper order does not change figures or their numbers. Reorder prose, references, and embedded figures freely. Paper displays the numbers chosen in Figure, and exports use those same numbers. Canvas list order is also separate from publication numbering.

Existing projects retain their reference keys and filenames. The readable title is not a filename, and you do not need to rename stored files to rename a figure.

Panels and captions

Exporting figures

The Inspector’s Export section renders the selected figure to PNG, SVG, or PDF. For submissions, expand Journal-spec raster, pick a target width (single/double column presets or custom mm), a DPI and transparency, and export TIFF or PNG at exact print size.

An export captures the figure when you start it, so edits made while choosing a filename cannot change its artwork or dimensions. Large raster exports offer Cancel export and keep the editor responsive. An unsupported output size reports an error rather than reducing its resolution. PDF pages use the figure’s physical dimensions.

Send to deck… turns the figure into a slide, still linked to the same plots.

Troubleshooting

Symptom Cause → fix
Ctrl+click won’t select a part The plot isn’t semantic (imported without its manifest) → re-save via fp.save and re-import, or check flux validate-plot
An import landed huge / outside the frame True-size import of a large plot → Ctrl+Shift+I to bring it inside, then resize deliberately
Restyles vanished after regenerating The plot’s series names changed in the script → keep series= names stable (see Semantic plots)
“These figures changed on disk” banner Another tool or agent edited them → Reload theirs or Overwrite with mine — nothing is lost silently
“Some figures could not be loaded” A referenced canvas is missing or unreadable. Restore or repair it and reopen the project; saving is blocked to preserve the existing files.
“Caption edits conflict” Both the caption and its Markdown copy changed. Reconcile those versions before saving; changing panel labels alone does not create an external edit.

For 3D model problems (grey tiles, Orbit, missing GLB files), see 3D models troubleshooting.

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