Generates detailed 3D models of anatomical structures from medical images such as CT scans.

What it does

Technology behind the scenes

Supported inputs

NIfTI (.nii, .nii.gz), NRRD, MHA, DICOM ZIP archives (multi-series/study allowed)

Outputs

Important note

Take steps to anonymize your data ahead of time. We cannot guarantee complete anonymization and are not liable for any data you upload. If you plan to make raw data available, verify that the copy anonymized by NIH 3D contains no identifying information before making it public.

Prepares and standardizes 3D mesh files for NIH 3D visualization, sharing, animation, and 3D printing.

What it does

Supported inputs

.glb, .stl, .obj, .fbx, .x3d, .wrl, .3mf, .ply, .blend; ZIP with FBX + textures; ZIP with OBJ + MTL + optional textures

Outputs

Not Intended for 3D Printing

Intended for 3D Printing

Models prepared for 3D printing may also receive .ply, .wrl, .3mf, and .stl outputs.

Preview PNG images and packaged texture files are generated when applicable.

Output Format Attributes

3MF File Support

Not supported:

File Size and Output Limits

Output format limits

When a processed mesh is very large, certain output formats are omitted:

Reducing Large 3D Files

Very large or highly detailed 3D models can be slow to upload, open, process, and display. Files approaching or exceeding 1 GB are especially likely to cause problems in automated workflows.

File size alone does not tell the whole story. Different file formats store and compress 3D data differently, so models with the same geometry can have very different file sizes. For this reason, consider both file size and triangle count.

As a practical guide:

These are guidelines rather than hard limits. A simpler model is usually preferable if it looks the same at the intended viewing or printing resolution.

In ChimeraX

Whenever possible, reduce the surface before exporting.

For volumetric or density-map surfaces:

Increase the step (2, 3, 4, etc.) until the surface is as simple as possible while retaining the detail you need.

For molecular surfaces:

Increasing the grid spacing produces fewer triangles and smaller exports. Larger values create fewer triangles and smaller exported files. Values around 1 Å are often a reasonable starting point for visualization.

In Blender 5.1

If the model has already been exported, use the Decimate modifier:

Alternatively, decimate the mesh directly in Edit Mode:

Unlike the Decimate modifier, this method changes the mesh directly, so save a copy of the original first.

Files approaching 1 GB or models containing several million triangles should generally be reduced before submission. Compression or a more efficient file format may reduce the stored file size, but it does not reduce the underlying geometry that must be loaded and processed.

Smooth the Appearance After Decimation

After reducing the polygon count, a surface may look more faceted. Blender can smooth the surface normals so the model appears smoother without adding polygons.

In Object Mode:

This is useful for visualization, because it improves how light is interpolated across the surface without increasing the triangle count.

Automatic decimation

For ChimeraX files and files that were successfully repaired, if the GLB output would exceed 300 MB the mesh is automatically decimated before export. The reduction targets the largest objects most aggressively while barely touching small objects. Vertex colors are preserved through this process. After decimation, the polygon thresholds above apply to the reduced mesh, so WRL and X3D outputs may still be generated for files that would otherwise have been too large.

Decimation does not apply to unrepaired mesh file uploads or to files where repair was attempted but failed.

ChimeraX files

For ChimeraX-generated files, additional size-related limits apply internally to the repair and analysis pipeline. Very large ChimeraX meshes may receive less precise repair strategy selection, and some quality metrics used in repair routing are skipped above certain polygon counts. Output format availability follows the same rules as above.

Analyzes geometry, attempts increasingly robust repair strategies, and clearly identifies cases where a verified repair could not be produced.

What it does

Repair strategies

Repair methods are attempted from least to most aggressive and stop once a valid result is produced.

Disconnected pieces

We intentionally keep loose objects to preserve intentional multi-part models or floating components, though this can sometimes capture debris. Pieces appear as different colors in the GLB file for easy identification. Use the NIH 3D Viewer's wireframe mode to see enclosed pieces that could also be removed. Hide unwanted pieces, then export as STL for printing (you can add struts to support floating pieces), or edit in your own 3D software. You may wish to upload your manually cleaned file as a supplementary input.

File suffixes

A print_caution model may still be printable, but printability will be printer and slicing software dependent. The same applies for anything output from NIH 3D.

Important limitations

Always inspect the output. If you're not satisfied with the repair result—such as unwanted merging or other issues—you can turn off mesh repair and instead use “intended for 3D printing” after manually repairing the mesh with tools like Blender's 3D Print Toolbox, Autodesk Netfabb, or other available repair software.

Generates detailed 3D visualizations of molecular structures for 3D printing, web visualization, and downstream analysis. Structures are processed inside ChimeraX using the NIH3D custom presets. The resulting files then pass through a mesh processing pipeline that prepares them for the web viewer, 3D printing, and download.

Supported inputs

.cif, .cif.gz, .pdb, .pdb1, .ent, .mol, .mol2, .sdf, .mae, .map, .map.gz, .omap, .tif, .tiff

Quick Submit

Models can also be generated directly from supported database identifiers without manually uploading a structure file.

Supported databases

Processing pipeline

After a structure file is opened in ChimeraX, the pipeline automatically classifies it into one of four treatment types and applies the corresponding visualization steps.

Small molecules

Structures with no named polymer residues (e.g., PubChem compounds, ligands) are rendered in three representations: sticks, CPK space-filling, and ball-and-stick. Each is produced in both a colored and a monochrome variant. All small molecule outputs are printable geometry — no smooth normals are applied. They will appear faceted on screen at low polygon counts, but enabling smooth normals in Blender will improve their appearance without affecting print quality. Small molecules are also the best case for automated repair — the geometry is composed of overlapping closed spheres and cylinders that merge cleanly and quickly.

Macromolecules — medium

Structures with polymer chains below ~250,000 atoms. Two representation families are produced:

Macromolecules — large

Structures with polymer chains above ~250,000 atoms. A reduced set of surface outputs is generated (monochrome and by-chain; hydrophobicity for structures below an upper size cutoff). Ribbon outputs are skipped for performance.

Density maps (EMDB)

Volumetric electron microscopy maps are isosurface-rendered at the deposited contour level (Quick Submit) or by the contour level provided by the user (Regular Submission). Two coloring variants are produced: monochrome and radial gradient (surface colored from center outward).

AlphaFold structures

The most output-rich treatment. In addition to all the macromolecule representations, AlphaFold outputs include:

When the structure contains a well-defined high-confidence core (a connected set of residues with pLDDT > 50 that is structurally distinct from the rest of the model), outputs are generated for both the full model and for that high-confidence subset independently.

Output filename conventions

Every submitted structure produces a set of files whose names encode the structure source, representation, geometry profile, and coloring. Following the ID, the file name generally breaks down into four parts: -prefix-representation-coloring-repair. Not every entry includes all of these parts, as described in more detail below. For example, an AlphaFold entry might look like -all-ribbon-thin-rainbow, while a PDB entry might look like -ribbon-thick-print_struts-repaired.

AlphaFold confidence prefix

Representation

Coloring

Print vs. visualization geometry

Printable outputs (-thick-print_struts, -highres-) are designed to survive physical 3D printing:

Visualization outputs (-thin-, -lowres-) are optimized for web and real-time display:

Small molecule outputs are printable geometry and do not have smooth normals applied, so they may appear faceted on screen. To improve their appearance for display purposes, enable smooth normals in Blender: select the object, right-click in the viewport, and choose Shade Smooth. This does not affect the underlying geometry or print quality.

Mesh processing and repair

After ChimeraX produces the visualization files, each one passes through a mesh processing stage. The route taken depends on the representation.

Printable nocolor outputs go through full geometry repair. The pipeline attempts to produce a watertight, manifold mesh suitable for slicing and printing. Ribbons are remeshed using a voxel-based approach; small molecules are boolean-unioned from their component spheres and cylinders. Successfully repaired files are marked -repaired in the filename.

Printable colored outputs are exported without repair. Repair requires converting geometry through an intermediate format that cannot carry vertex colors, so the colored variant is passed through as-is and marked -print_caution. The corresponding nocolor sibling is the repaired version intended for actual printing.

Visualization outputs are prepared for display and export formats without geometry repair.

What the suffix tells you

Missing outputs

Some representations are skipped when the structure or its data cannot support them. Known conditions include:

As long as at least one representation is produced successfully, the entry will not be marked as failed. If you notice an expected output is missing, reach out and we can review the processing logs together.