3D models in Flux

Import a model#

Import a GLB mesh through Import, drag it onto the canvas, or pick its 3D tile in the gallery. Flux keeps a project copy, so sharing the project does not depend on the original file. A plain GLB supplies geometry and colours. A 3D fluxplot also supplies named parts, physical size, axes, labels, value fields and optional shapes through the matching .fluxplot.json file. Keep that file beside the GLB when importing. An invalid, newer or mismatched manifest produces a warning and leaves the geometry available as a plain mesh.

3D models need a saved project. In a project you have not saved yet, importing a GLB first asks you to save it; then the file picker opens again, so pick the files a second time. Cancelling that second picker keeps the saved project. Dragged-in files need no second pick. If preparing a model takes more than a second, a notice names the files still being imported. A placed model shows a dashed outline while its image is prepared, and “Preparing 3D preview” only if that takes longer than a second.

Create a 3D fluxplot in Python#

In Python, start a scene, add your mesh and save it into plots/. This needs a fluxplot release with fp.scene3d; install or update fluxplot if needed. 3D plots covers scenes, value fields and shape states in depth.

import fluxplot as fp

# vertices: an N×3 array of coordinates
# faces: an M×3 array of vertex indices
sc = fp.scene3d(figsize=(3.5, 3),
                units="µm", up="z",
                axes="triad")
fp.mesh3d(sc, (vertices, faces),
          series="neuron",
          color="#4385be")
sc.view(azimuth=30, elevation=20)
fp.save(sc, "plots/neuron")

figsize is in inches; up describes your data coordinates. The gallery inserts that physical size. In a trusted notebook, displaying sc opens the interactive viewer. Use Copy view and paste the sc.view(...) line it produces into your code, then save to make that angle the scene’s Home view. In the viewer, click the model (or hold Ctrl) before scrolling to zoom; otherwise scrolling moves the notebook as usual. For a static output, use sc.show(static=True).

Update from source#

After rerunning Python, Source changed appears in the Inspector and as a dot in Layers, together with Update from source. Choose it to accept the new geometry and metadata. Your box, camera and look stay in place; restyles and field settings remain for surviving part IDs, and shape weights remain for surviving names. Flux warns when parts disappear or bounds move substantially. Undo restores the previous stored model. Source changes never replace the model automatically. A missing original file leaves the saved copy available. For a recipe-backed model, Regenerate in X-ray reruns the recipe with its parameters and applies the same update after it succeeds.

Orbit and views#

Double-click the mesh, or choose Orbit in the Inspector, to turn it. While you orbit, the button reads Done and a hint over the model lists the keys:

Clicking outside the model also finishes. Space+drag and Ctrl+wheel return to canvas navigation. Double-clicking a label, colorbar, legend or scale bar selects that part instead, as with a 2D plot’s parts.

The 3D model panel#

The Inspector’s 3D model panel is grouped into sections:

• 3D view: Orbit, the camera numbers, the view buttons Front, Back, Right, Left, Top, Bottom and Home (each shows its key), and Projection (Ortho or Persp).
• Appearance: Colours is From file (the mesh’s own colours) or Uniform (one Model colour, shown only for Uniform); Lighting is Studio or Unlit.
• Value fields and Shape, when the model has them (see below).

Resizing the box reframes the model while labels keep their physical type size. A physical scale bar is shown only in orthographic view. The default view fits the model snugly; with box axes it fits the whole axes box, so ticks and labels stay inside the frame. Looking almost straight down one axis shrinks it to a short stub. Its tick labels are then hidden rather than stacked on top of each other, and so is its title if the title is longer than the stub. The axis line, ticks and grid stay.

Parts, value fields and shapes#

Use Alt+R for the model’s X-ray. Named mesh parts can be recoloured, hidden or made transparent; labels can be restyled independently. Mesh-part colours show while Colours is From file, so painting a mesh part on a Uniform model switches it to From file (one undo, with a notice). For a continuous value field, change its colormap and Min / Max under Value fields: the mesh and colorbar update together, without rerunning Python. A part colour overrides its value field; Reset part colour restores field colouring.

If the GLB has named shape states, Shape offers live weights from 0 to 1. A sequence instead starts with a Frame control: 0 is the base, 1 onwards are the saved shapes, and fractional values blend neighbouring frames. Custom means the current weights are not a sequence frame. Reset shape restores the saved weights. Stored scientific weights can extend beyond the slider range.

Export and limits#

PNG and TIFF exports rasterize the result at the requested print size. SVG and PDF keep the mesh as a high-resolution image while axes, labels, legends and scale bars remain vector artwork. Paper uses the saved figure view in its embeds and document exports. Large meshes can be reduced at creation with fp.mesh3d(..., max_faces=...); this uses the optional fluxplot[mesh] extra. Texture images are omitted and skinning is ignored: Flux shows the stored mesh geometry, so bake a desired pose before exporting the GLB. Point and line primitives are refused; export triangle meshes.

Troubleshooting#