How to build a virtual patient in Cympha Studio

A virtual patient combines CBCT, intraoral scans, a facial scan and photos in one registered scene in Cympha Studio, saved as a .cyp bundle for the dental case.

Audience: Orthodontists, oral surgeons, prosthodontists, and lab designers who need a single 3D scene that holds CBCT, intra-oral scans, a facial scan, and reference photos for the same patient — all aligned in one coordinate frame.

You'll come away knowing: how to load each modality into Studio, how to align it to the others using Register to…, what successful registration looks like, and how to save the assembled scene as a .cyp bundle you can reopen later.

Time required: Around fifteen to twenty-five minutes per patient the first time. Half that once the workflow is muscle memory.

Before you start

You need:

A CBCT series as a folder of DICOM files (one series, not a multi-series export).
One or more intra-oral scans (.stl, .ply, or .obj). Upper and lower arches are usually separate files; a .ply with UV coordinates and a paired .png / .jpg is the most reliable textured format. .stl is geometry-only.
(Optional) A facial scan mesh — same formats as intra-oral.
(Optional) Reference photos (extra-oral, intra-oral, smile shots) as .png, .jpg, .jpeg, or .webp.
A wide browser window. Some Studio controls (the staging chart, the IPR toggle, the Remove region mesh tool) only appear at desktop widths (~1024 px and up).

Open studio.cympha.com — no account or sign-in is needed for anything in this workflow — and confirm you're starting from an empty viewer. If a previous case is lingering, open the hamburger menu (☰) at top-left and click Clear scene. Only Clear scene removes everything; opening a new file only replaces its own layer.

Workspace tip. Use the top-bar Workspace nav to pick a context that makes Studio's menus appropriate for what you're doing. 3D Processing is the broadest workspace and the safest default while you're assembling a virtual patient. Facial Scan narrows the menu to DICOM + scan + facial scan + pictures, which is handy if you're focused on face-to-bone alignment.

Step 1 — Load the CBCT first

The CBCT is the anchor. Every other modality will be registered into the CBCT's patient coordinate frame, so load it first.

Click ☰ → Open DICOM….
Choose the folder containing one CBCT series (folder picker, not file picker).
Wait for decoding. When the volume is ready the slice row appears at the top of the viewport and a 3D rendering of the volume appears in the main view.
Open the View tools panel — click the small rendering icon on the left-hand floating dock that appears once CBCT is loaded.
Adjust HU threshold until bone and teeth separate cleanly from soft tissue. The slider runs roughly −1024 to 2048 HU; somewhere between 200 and 500 HU is a good starting point for separating bone.
Adjust Opacity (0–1) if the volume looks too solid or too washed out.

Cloud plan prompt. If implant plans are stored in your Cympha cloud for that CBCT series, Studio may offer to import one after the DICOM finishes loading. If you're not doing implant work, dismiss it and continue.

Step 2 — Add the upper arch scan

☰ → Open optical scan file… (or use Add model on the top toolbar — same effect).
Select the upper arch mesh. If you have a textured .ply plus its .png/.jpg image, Ctrl-click both in the file picker so the image binds as a UV texture.
The mesh loads into the same 3D view. It will arrive in scanner coordinates — almost certainly floating off to the side of the CBCT volume.

Multiple meshes at once. You can select several mesh files in the same picker (no images in that selection) to load them all in one step. Don't mix one mesh with multiple textures — that's not a supported combination.

Step 3 — Register the upper arch to the CBCT

Cympha's registration is rigid (rotation + translation, no scaling or shear). You pick at least three matching landmark pairs and Studio computes the transform that best maps the source mesh onto the target.

Right-click on the upper arch mesh in the 3D view to open the context menu.
Choose Register to…. The Register model panel opens and Studio enters a strict alternating-pick mode. The source mesh becomes the only visible layer for source picks; the scene returns to a snapshot of what was visible at start for target picks.
Place pair 1. Left-click a clear landmark on the upper arch — say the mesial buccal cusp of the upper right first molar. A reddish marker sphere appears. Then left-click the matching anatomy on the CBCT volume. Studio walks the view ray into the volume and places a greenish marker on the first voxel at or above the HU threshold; the panel shows CT (DICOM) as the target.
Place pairs 2 and 3. Pick anatomy that's well-spread — for an arch, that means one landmark on each side and one anterior, not three clustered in the same quadrant. Clustered landmarks let the rigid solve slide along flat regions.
Watch the Pairs counter climb. With three or more complete pairs, Register lights up.
If you fluffed a pick before reaching three pairs, press <kbd>Delete</kbd> (forward delete, not <kbd>Backspace</kbd>) to remove the last marker. After three pairs delete is locked — use Cancel to wipe all picks and start over.
Click Register. The arch snaps into the CBCT's coordinate frame.

After a successful CT-targeted registration, turn on Show in 2D for the registered mesh (right-click menu) so its silhouette appears in MPR overlays — quick verification that the alignment looks anatomically sane on axial / sagittal / coronal slices.

Register vs Cancel vs Close. Register applies the transform. Cancel restores the source mesh to its pose at the moment registration started — use this when picks were wrong. Close dismisses the panel without applying and without rewinding — use this when you opened registration by accident.

Step 4 — Add the lower arch scan

Two ways:

Option A — independent register. Repeat Steps 2 and 3 with the lower arch file. Register it directly to the CBCT using bony landmarks (mental foramen, mandibular symphysis, ramus features) plus dentition. This is the cleanest option when you trust the CBCT segmentation.

Option B — register to the upper arch.

Load the lower arch with ☰ → Open optical scan file… (or Add model), as in Step 2.
Right-click the lower arch → Register to…, and pick landmark pairs against the already-aligned upper arch instead of the CBCT — occlusal contacts and interdigitating cusps make good pairs when the scans were taken in occlusion.
Click Register. The lower arch lands in the same patient frame via the upper.
Optional — double-click the lower mesh to open the positioning gizmo and movement panel for fine bite adjustment, or run Register to… again against the CBCT to refine.

Option B is convenient when the two scans were taken in occlusion; Option A is more rigorous when the scans were taken separately.

Step 5 — Add a facial scan (optional)

☰ → Open optical scan file… (or Add model), pick the facial mesh.
Right-click the facial mesh → Register to….
Pick three or more bilateral and midline landmarks on the face (e.g., right exocanthion, left exocanthion, soft-tissue nasion, subnasale) and match them to the corresponding CBCT soft-tissue features. With the CBCT HU threshold dropped to soft-tissue range, the rendered face is pickable in the volume.
Register.

Visibility snapshot. When you start registration, Studio saves which layers were visible. During target picks it hides the source mesh and restores other layers to that snapshot. If the CBCT was hidden when you began, target picks can't hit it — turn the CBCT back on before Register to….

Step 6 — Add reference pictures

These are gallery-only — they don't bind to a mesh as a UV texture.

☰ → Add pictures….
Multi-select .png, .jpg, .jpeg, or .webp files (extra-oral photos, smile shots, OPG screenshots).
They appear in the Media gallery (pictures icon on the top toolbar). You can add a comment per picture; the comment is stored with the project.

Studio's Screen capture button (camera icon on the top toolbar) is also useful here — it saves the current viewer layout as a single PNG (including MPR slices when the CBCT layout is active) and prompts for an optional comment. The filename is timestamped. The capture lands in the same gallery.

Step 7 — Save as a `.cyp` project

You've now assembled the virtual patient. Save it so it survives the browser tab closing.

☰ → Save project as….
On Chrome or Edge you'll be asked to pick a folder. Studio writes <FolderName>.cyp plus a sibling <FolderName>_CypFile asset folder. Project pictures land under <FolderName>_CypFile/Pictures/.
On other browsers Studio falls back to a downloaded archive.

To reopen later, ☰ → Open project… and pick the same folder. Studio restores meshes, the CT, the registrations, implant plans if any, and the gallery (with comments).

What success looks like

The CBCT volume and all registered meshes share a single coordinate frame — rotating the camera moves them as one rigid scene.
The arch silhouettes overlay sensibly on axial / sagittal / coronal MPR slices (turn Show in 2D on for each mesh if not already on).
Cycling through standard views (front / right / left, available on the arch toolbar when a .gvw case is loaded, or via Reset camera otherwise) shows teeth, bone, and facial soft tissue in coherent registration.
Saving as .cyp and reopening in a fresh tab restores everything including pictures and comments.

Troubleshooting

The Register button never lights up. You need at least three complete pairs (six picks, alternating source/target). Watch the Pairs counter — it shows min(source count, target count). If you only see source markers, you're skipping the target click.

The arch snaps to a wildly wrong pose. Almost always a landmark mismatch: the source pick and the matching target pick are on different anatomy. Clustered landmarks (all three on one molar quadrant) cause similar instability. Cancel the registration, then redo with landmarks spread across the arch.

I can't pick the CBCT during a target step. The visibility snapshot taken when registration started doesn't include the CT. Press Cancel, turn the CT back on (View tools panel — bump opacity above zero, set a sensible HU threshold), then run Register to… again.

The texture image didn't bind to my mesh. STL files don't carry UV coordinates, so an STL + image combination won't texture. OBJ files often lack the UVs that this pipeline needs. .ply with UVs is the most reliable format. Re-export with UVs from your scanner.

I right-clicked a case tooth and Register to… is missing. Registration is only offered for user-added meshes. Case geometry (tooth meshes that came in with a .gvw plan) carries case metadata and can't be moved with Register to… — that protects the plan.