About NIH 3D
The NIH 3D is an open, comprehensive, and interactive website for searching, browsing, downloading, and sharing biomedical 3D models (meshes) for 3D Printing, AR, VR, illustration, animation, 3D interactive, and other purposes. "Biomedical" includes models of cells, bacteria, or viruses, molecules like proteins or DNA, and anatomical models of organs, tissue, and body parts.
NIH 3D is a complete rebuild of the NIH 3D Print Exchange (3DPX)
With the NIH 3D Print Exchange (3DPX), we wanted more people to use 3D printing for science, but we couldn’t find a resource dedicated to that. We had a lot of scientific models that we knew other people could benefit from, but we didn’t have a good way of making them available. With NIH 3D we are expanding the scope of models in our collection to include those for AR, VR, animation, and other 3D applications.
Everyone! NIH 3D caters to a wide variety of users with varying levels of experience with 3D technology. It is particularly meant for:
- Researchers – scientific and clinical researchers will benefit from visualizing molecules, organisms, and anatomical parts
- Educators and students – NIH 3D will provide models that are useful as hands-on teaching aids, and some models will have supplemental materials for teachers to use in the classroom
- Presenters – anyone presenting on biomedical or bioscientific work who wants to help their audience visualize the concept they are communicating
- 3D printing enthusiasts – NIH 3D offers tools that allow users to easily generate and refine models from a wide range of file types.
The NIH 3D is unique because:
- It is dedicated specifically to bioscientific 3D prints.
- It is the first government-sponsored website dedicated to 3D printing.
- It includes new, sophisticated, and free tools to convert scientific data into printable objects in only minutes.
- Part of our mission is dedicated to advancing the use of 3D technology in STEM education, so we will encourage users to add classroom worksheets and other supplements so that the prints can be used as hands-on teaching aids.
The Basics of 3D Printing
3D printers create solid objects by building up thin layers of material (such as different types of plastic); think of a normal printer printing a “stack” of paper but in a predefined shape – it can be solid or hollow, and sometimes needs support scaffolding to hold up pieces of the print when printing.
There are many different kinds of materials and technologies used in 3D printing. Some are:
- Plastic – uses a nozzle like a glue gun to melt plastic into thin filaments that are layered (aka thermoplastic extrusion, fused deposition)
- Binder jetting – uses a bed of plaster powder where an inket-style print head lays down binding solution (similar to superglue); alternates layers of powder and binder
- Metal – many ways to use different metals, can use heat, lasers, electron beams.
- Stereolithography – uses resin that is layered and cured by lasers or lights
The most common and universal file formats for 3D printing are STL and VRML. STL stands for “stereolithography” – it is a 3D rendering that contains only a single color. This is typically the file format you would use with desktop 3D printers. VRML (“vermal”, .WRL file extension) stands for “Virtual Reality Modeling Language” – it is a newer digital 3D file type that also includes color, so it can be used on desktop 3D printers with more than one extruder (i.e. two more nozzles that each can print with a different color plastic), or with full-color binder jetting technology.
Additive Manufacturing File Format (.AMF) is a new XML-based open standard for 3D printing. Unlike STL, it contains support for color. They can also be compressed to about half the size of a compressed STL file. AMF is not widely used at present, but in future we would like to add this an option for uploading and downloading files to and from the NIH 3D.
Another file format input for 3D printers in GCode. This file contains detailed instructions for a 3D printer to follow for each slice, like the starting point for each layer and the "route" that the nozzle or print head will follow in laying down the material. In addition, 3D printer manufacturers may have their own proprietary input file formats that contain instructions specific to the methodology for that make or model, and that are compatible only with that manufacturer's software. This does not create a barrier to printing with these machines, as the proprietary file format is generated from the user's own STL or WRL file. Some examples include the .form file, used with the PreForm software for Form1 printers, or the .zpr format, proprietary to the ZPrint and ZEdit software used with ZCorp binder jet printers.
Just about anything can be 3D-printed, and our focus is only on those items that are bioscientifically relevant, such as models of molecules, organs, and lab equipment. We moderate our content regularly to prevent inappropriate material from being shared, and will remove users should we find that they’re misusing the resource.
Only registered users can share models by going to "Submit a Model." Registration is free and open to everyone. Once you are registered and logged in, you have two options:
1. The "Quicksubmit" feature allows you to enter a database accession code for a structure from an external repository to automatically create 3D Mesh files. This works for files from (1) the Electron Microscopy Databank (EMDB) (2) the Protein Data Bank (PDB) ; and (3) the NCBI PubChem small molecule structure database .
For electron microscopy density maps of macromolecular complexes and subcellular structures from the EMDB, you will need to enter the 4- to 5-digit numeric code from the file in the EMDB repository, found in the URL format http://www.ebi.ac.uk/pdbe/entry/EMD-[emdbID]. For example, for the Structure of immature Dengue virus at low pH, we see from the URL and on the resulting page that the accession code is "5006." Enter this code into the Quicksubmit box with the drop-down for "EMDB ID" to generate a 3D-printable version of this virus.
For biological macromolecular structures from the PDB, you will need to enter the 4- or 8-digit alphanumeric code from the file in the PDB, found in the URL format http://pdb.org/pdb/explore/explore.do?structureId=[pdbID]. For example, for the Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor, we see from the URL and on the resulting page that the accession code is "1TV5." Enter this code into the Quicksubmit box with the drop-down for "PDB ID" to generate
For small molecule structures from PubChem, you will need to enter the numeric chemical ID ("CID"), which is an integer between 1 and 15 digits. This can be found in the URL format https://pubchem.ncbi.nlm.nih.gov/compound/[CID]. For example, for theobromine, we see from the URL and on the resulting page that the CID is "5429". Enter this code into the Quicksumbit box with the drop-down for "PubChem"
2. You may upload a file:
You may share 3D mesh files that you have generated in glb, x3d, stl, or wrl format. We will convert any input mesh file into these 4 output formats (note: there may be loss of textures and other details in the file conversion, but your original file will not be modified). Note: Our 3D viewer presents the glb file created by the entry. At this time, our 2D renderings are not presenting textures, but the 3D viewer will show them correctly if they were part of an input glb file.
You may also opt to upload one of several scientific data formats (eg. pdb, mol, sdf...) which can be processed by our workflows into 3D Printable and non-3D-Printable representations in x3d, wrl, stl, and glb format. Many of these models have vertex color assigned.
All users can download models on the database; most are freely available to use in whatever way you’d like, but some authors might want to protect their models with Creative Commons licenses to define how others can and cannot use their models. All models submitted by NIH and other government agencies are public domain, and have no restrictions.
When sharing a model on the database, you can select a Creative Commons license to allow or restrict how users can share, remix, or modify your models. At this time we do not allow users to reserve copyright on their models, to facilitate open science and open data sharing.
Our free, online web tools will automatically convert your file to a format that is readily compatible with 3D printers if you select the "mesh repair" option.
A Version is created when you "edit" your model entry. If you change a file or setting that requires the workflows to be rerun and new models to be generated, the version will increase by 1.0. If you change the title, description, or other textual data that doesn't require new models to be generated, the version will increment by 0.01. This system has been implemented such that when users download models or referene them in publication, there is a record of any changes that have occured since the user last visisted.
If you have used an entry on NIH 3D to iterate a new design, your new model is a "Remix".
Creating 3D Models
Any medical imaging file has the potential to contain personal health information (PHI) and personally identifiable information (PII). When you upload an accepted medical imaging format to NIH 3D, all stored PII/PHI will be stripped from the file. If you opt to may your raw DICOM data available from our anatomy workflow, or if you add medical imaging to your supplemental files, we flag these entries for review by an NIH 3D moderator before they can be published to ensure that these files do not include imaging of the entire face which could potentially identify a patient.
Blender, SketchUp, OpenSCAD, Netfabb basic, and FreeCAD are among the free, open source modeling software that you can use to design 3D models. Visit our page with Additional Resources to learn more.
PubChem generates theoretical 3D confomers using a program called Omega, and NIH 3D draws that information from PubChem to generate a 3D model. Conformer generation is computationally intensive, and PubChem cannot generate 3D conformers for large and complex chemical structures. This effects approximately 12% of all PubChem entires. You can still generate a 3D model of the molecule using a workaround; download the 2D SDF of the molecule from the PubChem site, use Omega or Avogadro software to attempt a 3D reconstruction, export a 3D file in CIF, MOL, PDB, or SDF format, and upload the file to NIH 3D through "Submit a Model"
Our free, online web tools will automatically convert your file to a format that is readily compatible with 3D printers if you select the "mesh repair" option.
Using 3D Models
We don’t offer general printing for the public, but there are plenty of online or brick-and-mortar stores to choose from. You can also check your local library or area schools.
Model files are downloaded in GLB, X3D, STL or WRL formats.
GLB is the binary version of glTF format . It is used extensively for web3D applications
Extensible 3D (X3D) Graphics is the royalty-free open standard for publishing, viewing, printing and archiving interactive 3D models on the Web. X3D and HAnim standards are developed and maintained by the Web3D Consortium.
WRL is a format that is commonly used for color 3D printing. We recommend .wrl files specifically for those wishing to print in COLOR using a powder bed printer.
STL is a format that is commonly used for monochrome 3D printing. It is widely used by 3D printers of all types and is also broadly recognized by other 3D software packages.
All of these files can be opened with the free 3D modeling software Blender or MeshLab . STL is well supported in most 3D applications, but the others have varied support and may require specialized plugins.
When a 3D model is created, there can be errors that will prevent it from printing properly. Holes in the mesh, inverted normals, unconnected borders, and intersecting faces can all cause print failures. To increase the printability of models on the NIH 3D, a service called Netfabb is used to clean and repair .stl files. Netfabb works by running an analysis on the model, and then performing steps to repair any problems it finds. Netfabb will fill holes, correct triangle orientation, merge close borders, delete redundant and degenerate faces, and remove self intersections. A resulting model that is verified as clean, watertight and printable is returned to NIH 3D, and is made avaliable for download on the model page. Mesh repair is run on all NIH 3D-generated molecular .stl outputs which are intended for 3D printing. For DICOM, .map, .omap, .x3d, .wrl, .glb, or .stl uploads we leave it to the discretion of the user as to whether to run this step as it can be time-consuming and will fail if the model is not appropriate.
Generally, "Optimized for 3D Printing" means that either NIH 3D or the owner of the model has indicated that the model can be 3D printed.
For molecular models generated by NIH 3D, this specifically means that the models are mechanically sound when printed on an appropriate printer. The "appropriate" printer depends on the file type. Our .wrl files are intended for use printing in COLOR on a powder bed printer. They have not undergone mesh repair and will likely fail on other printer types.
For all non-color 3D printing applications, we recommend .stl format files. Those tagged with -mr (eg. 3nir-ribbons-nih3d-mr.stl) have been run through the mesh repair system described above and should be compatible with most printers.
This depends on the license that has been selected for the entry. Many entries have a fairly open CC-BY or Public Domain license, but NOT ALL do. It is important to note the license and attribution instructions that the user has provided to ensure you are not violating our terms and conditions.
Interactive 3D Viewer
No. We’re using technologies called WebGL, Babylon.js, and glTF that are designed to work in web browsers without special software. Some NIH 3D models are very large and may take several minutes to load, particularly with slower connections.
WebGL is a cross-platform, royalty-free web standard for viewing 3D graphics in a web browser. WebGL technology allows users to view interactive 3D content without the need to install a special plugin. Visit the WebGL home page to find more.
Information for NIH Staff
The NIH Library, based in Building 10 on the NIH main campus, hosts a 3D Printing service through its Technology Sandbox .
There is a Special Interest Group (SIG) on 3D printing, and you can join the listserv to find out news and events. Search the NIH website to find out how to sign up for a SIG or an email list.
A DOI (Digital Object Identifier) is a unique alphanumeric identifier assigned to digital or online resources, ensuring their distinctiveness, permanence, and accessibility. It serves as a standardized reference for scholarly articles, research data, and other digital objects, aiding in proper citation and attribution. DOIs are associated with metadata containing resource details and are widely supported across digital environments, making them a reliable means of accessing and referencing digital content.
NIH 3D partners withDataCite to create DOIs using information that users share during the DOI request process. Certain information, including creator and organization names, are required by DataCite to fulfill the request.
We automatically assign DOIs to all published models that are generated using Quick Submit workflows. However, for models that are created by uploading files, our administrators will manually review each request before approving it for DOI assignment.
The DOI is specifically assigned to encompass only the input and output files, if they are present, and does not encompass supplementary files or associated metadata.
Since the Quick Submit process relies solely on data from PDB, EMD, or PubChem and does not involve user-provided data, NIH 3D assumes creator rights because it oversees all the creative and technical aspects of entry creation.
If your entry is derived from data processed by NIH 3D, we are listed as the creator because we are solely responsible for translating this data into a 3D model. All creative and technical processes involved in this transformation are provided by NIH 3D.
Your DOI corresponds to the major version of your entry at the time the DOI request is made. If you need to implement modifications that affect the input/output files, you must request an update for your existing DOI. Minor alterations to your entry, such as text or metadata changes, do not warrant a new DOI.
NIH 3D uses records from the Research Organization Registry (ROR) to list affiliations in the DOI request form. If you do not see your organization listed, you can suggest a new record using theROR Request Form on their website.