The Best Software for Medical 3d Animation: Is There One?

The best software for medical 3D animation is…not so fast.  Having studied in school and used for work 3D animation programs such as Maya and 3DS Max, and a number of other programs to create medical 3D animations over the years, I can honestly say that this is not a simple question to answer.  In fact, for each of my animations I use several pieces of software, depending on the animation.  In some cases this is a requirement, and in other cases its just makes sense to make the workflow faster and easier.



Let’s get into what these software packages are, what each one brings to the pipeline and how they compare.

First let’s realize that “medical 3d animation” is a subset of “general 3d animation”.  This means that you can use many of the same tools created for 3d animation.  There are some extra tools you may need for this type of 3d animation but more about that later.

Now lets break down the commonly used term “3d animation”.  This is a general term for the process of creating animated movies. When people say 3d animation software, they are usually referring to the entire process which involves 3d modeling, texturing, lighting, rigging, animation, and rendering.  Depending on how large the company is, you may wear multiple hats.  If you do your animations on your own, you may have to do all these tasks yourself.

Let’s get into the software tools that may fall under the umbrella of 3d animation.

Previsualization Software

Previsualization can have a few different forms.  It can be a storyboard, which can be drawn on paper or in Photoshop or Illustrator, and it can be an animatic, which is a simplified animation to block out the camera moves and shots. You do not necessarily need to use specific previsualization software (although they do exist, such as Toon Boom Storyboard Pro,  Moviestorm, Boords).

You can simply use your 3d modeling and animation program to build simple objects, animate them, and export to a package such as After Affects for editing, compositing and final output.

3D Modeling Software

Modeling Techniques

3D modeling is a large part of the full 3d animation pipeline.  Before we get into the software, lets talk about modeling techniques.  These can be divided into polygon, NURBS, subdivision surface, and “digital clay”.

Polygon modeling starts out with primitive objects made up of polygonal faces that are then built upon using various poly modeling tools such as extrusions.  You build the rough low poly shape of a model and then smooth it to make it organic or leave it unsmoothed to keep hard edges.

NURBS or Non Uniform Rational B Splines are very good at  modeling organic shapes.  These surfaces are created based on drawn curves and shape primitives which is what makes them good for organic modeling.  Curves can be revolved, extruded along another shape, projected onto a surface, etc.

Subdivision surface modeling involves a polygonal mesh that is subdivided several times and you can go back and forth between a low face count and a high face count object while modeling.

With digital clay, you are basically the closest to real life sculpting as you can be, with extra features you cannot even do in real life sculpting, such as tools that let you blow up a part of the clay object like a balloon or quickly clone it.  I’ve called it digital clay here to separate it from traditional polygon modeling, but it in fact is working with polygons just in a more intuitive way and with some technological advancements.

3D Modeling Programs

For medical 3d animation, you want a modeling program that is foremost great with organic shapes as well as inorganic hard surfaces.  This is because you will be doing a lot of organic modeling for anatomy, but objects such as medical devices and tools will require hard surface modeling.  You also want some sort of simple scripting language that will allow you to clone objects hundreds of times, place them all around a surface (think villi in an intestine), and perform other repetitive tasks to save you time.  If you are going to be using meshes from 3d reconstructions, your modeling software should have good cleanup and simplification tools for topology since reconstruction data, much like 3d scan data, is usually not clean or optimized for animation or texturing.

Maya and 3DS Max are the most popular 3d packages out there.  But they are not the only ones, and evolution of new technology brings us modeling techniques (and programs) which were not possible years ago.  Pixologic Zbrush comes to mind, as its more intuitive (and fun) clay like sculpting took the 3d modeling world by storm.  Up until then, modelers had to build their creations with points and lines and a mouse.  There was no such thing as “digital clay” using a pressure tablet.

I actually started with 3DS Max and “graduated” to Maya which was the more professional package.  They both had a steep learning curve compared to 2d programs like Photoshop, but this was understandable considering the amount of features and modules built into these packages.  After its acquisition by Autodesk, Maya actually had some more beginner friendly features added.

Both of these packages have modeling modules. Each one has its pros and cons.


NURBS in Maya are well developed.  Polygon and subdivision surface modeling toolsets are also present.  Maya is adding new features to its modeling toolset to compete with newer software like Zbrush, such as remesh to give extra detail to parts of your model, retopologize to reconstruct your models into clean quads, and more intuitive sculpting tools.

3DS Max

3DS Max used to be have a better modeling toolset than Maya in the past but now the difference has decreased.  3Ds Max is somewhat geared for games and architectural modeling.  It has polygon, subdivision surface, and spline based modeling.


Rhino is a 3d modeler that works with NURBS and polygons.  It is geared towards prototyping and fabrication.

Cinema 4D

Cinema 4D gives you the ability to do polygon modeling, modeling with splines, sculpting with digital clay, and boolean volume modeling.


Blender is program with an extensive modeling toolkit.  It also allows Python scripting.  It uses non-destructive modifiers to edit objects.  It does have digital clay sculpting similar to Zbrush but not as advanced.  It does have a learning curve.


Zbrush which I mentioned before makes high polygon sculpting very intuitive and thats part of its appeal for medical animation modeling.  The program is able to handle millions of polygons without crashing which allows smooth organic shapes at your fingertips without having to smooth and unsmooth.  The interface does take some getting used to and is geared toward pen and tablet use.  In addition, it does have an expanding hard surface modeling toolset..

Here is a video of modeling cranial nerves in Zbrush:

Having said all this, i mentioned earlier that I use multiple tools in my workflow.  This sometimes includes using multiple modeling tools if it makes things easier or faster.  The good thing is you can convert models between software packages.  For example, a workflow may involve building a low polygon object in Maya and then exporting it to Zbrush for high detail work, then exporting it back to Maya along with a displacement map for animation.

3D Animation Software

For medical animation, you should look for several things in a software package.   It should have a good system for keyframing animation and editing keyframes, and making the motion appear organic (for example random motion of proteins inside a cell).  Medical animation involves a lot of objects traveling along paths, dynamics/physics (you dont want to animate blood cells in a capillary by hand), constraints for having objects attach and detach, character animation tools for any animations involving humans or animals, and repetitive cyclical motions that an animation scripting language will help.  Blendshapes or morph targets are useful for animating between forms of an object, for example a growing embryo or facial expressions of a patient.

3DS Max and Maya both have animation modules built in.  So do a few other packages to an extent.

Maya is better suited for biological animation than 3DS Max due to its large assortment of advanced animation tools in addition to particles and dynamics which are useful in medical animation and can save you a lot of time.  You have various options for animating along paths.  In addition, its scripting language which is not tough to learn makes animating faster and gives you more possibilities than manually keyframing.  Blendshapes in Maya are easy to use.

Character rigging for animation is also more well developed in Maya without special plugins and you have various binding methods.   Animation bookmarks allow you to mark and organize events in time.  The software allows use of motion capture data natively.  You have a clip based, non-destructive, non-linear time editor at your disposal. Constraints are well developed and you have many types.  Since Autodesk purchased Maya it has introduced some ready to use setups reminiscent of 3DS Max but they can be used as a starting point for other work.

Here is a video of the creation of intestinal villi in Maya:

3DS Max does have fluid effects, morph targets, character animation and rigging tools, motion paths, particle flow effects and also 3rd party plugins you can buy.

Cinema 4D has some more advanced animation features including character animation, procedural animation and particle animation.

Zbrush animation is limited to basic transforms.

Compositing/Editing Software

Programs like Adobe After Effects and Adobe Premiere among others allow you to both non-linearly edit your animation timeline as well as composite various graphics together using alpha channels to form a multi layer final piece, similar to Photoshop but in motion.  This is essential for introducing elements into your final piece from different sources, where the backgrounds are removed.  When you watch a 3d animation of a medical device in action, its likely to contain various layers, for the device itself, background, live footage, etc.

After effects and Premiere work a little differently.  I find that After Effects is more flexible with effects and transformations and its better suited for shorter pieces including visual effects and motion graphics.  Premiere was originally created for video footage and is better suited for longer pieces.

The way you apply transformations is different, with After Effects being more intuitive and more advanced with a lot of flexibility and tons of options.

2D Animation Software

Medical and scientific animation commonly use two dimensional animation.  Some of the reasons are its more symbolic, easier and quicker to create, and not as memory intensive.


Macromedia Flash used to be the go to software for 2d animation creation both for standalone animations and web animations, until it was phased out.  It was replaced by Animate which has powerful 2d animation tools.  You can design your assets right inside the program with well developed illustration tools.

Character Animator

Character Animator software lets you import Ilustrator and Photoshop art and has some amazing features such as tracking your lips and facial expressions in real time when animating characters.

After Effects

Although not as powerful as some 2d animation specific programs, After Effects can hold its own when creating 2d animations, especially if you use plugins.  This makes it a good choice if you already have it for editing purposes.

Texturing/Painting Software

Texturing has always been a pain point in 3d animation especially with the layout of UVs for polygon modeling.  Things are easier with NURBS.  Most 3d animation packages have the applicable tools built in, for example a UV layout tool if the package has polygon modeling capabilities.

Both 3DS Max and Maya have well developed UV layout tools.  Zbrush has new intuitive texturing tools that make the process easier and more fun in addition to polypainting and its constantly being developed and more tools added.

The good news is even if you are using a certain animation package you do not have to use it for texturing or painting.  You can use external programs such as Substance Painter and then import the model back for animation.

3D Reconstruction Software

This is where the field of medical 3d animation differs from other animation fields, although in some fields such as forensic animation, 3d reconstruction is also used. However, in that case its usually to reconstruct a scene.  3D reconstruction software can be used for various purposes, such as the creation of a virtual model of a structure to be studied by students or colleagues in a 3d viewer,  an animation movie to be watched, or an interactive piece such as an anatomy atlas in the form of an app, educational game or website.

3D reconstruction in simplest terms is rebuilding a real structure in the virtual world.  This brings a new dimension to the animations as it is real life data that is shown visually in an animation which makes it accurate and this is important in the world of science.  In the world of biology and medicine, reconstruction is often done using two dimensional sections to build a 3d structure via some sort of segmentation.  There are several approaches to this and each one is based on the type of source data and modality used.

What you should look for in 3d reconstruction software is of course the ability to work with your chosen modality for importing data, good toolset for segmentation and an output to the appropriate 3d model file type for animation programs.


3D reconstruction from these modalities allows for the creation of 3d models of real data on a macro scale, such as the skull and any other body parts, human or animal.   It can also be used for smaller structures such as the parts of the brain.   This can be useful for animations as well as interactive and realtime pieces for medical illustration.


3D reconstruction from this modality makes it possible to reconstruct objects on a microscopic level, such as blood vessels, cells, neurons, and a multitude of others.  You are essentially creating 3d models for the world too small to be seen with the naked eye.  This is commonly done with fluorescent microscopy.

Back in the day we used to trace printed photographs from the microscope with a digitizing tablet which would give text files of coordinates and have to manually align them with pins.  3D reconstruction has come a long way since then.

3D Reconstruction Programs


This professional commercial software is used to reconstruct objects from MRI data as well as CT and 3D Microscopy.  Cells can be segmented from modern microscopes such as lightsheet to be used in animations and visualizations.

Amira is based on a system of nodes, similar in a way to Maya, where you connect a series of nodes to build a resulting output.


Imaris is a user friendly professional 3d reconstruction program that is available in different versions based on the use.  It is mainly built for reconstructions from microscopy such as confocal stacks.  It is able to read all the codes in a single image stack such as calibration, Z depth and resolution to produce a properly sized virtual model.  What makes it intuitive is the constant visual representation along with side and drop down menus.

Heres a quick video showing how 3d models are built in Imaris from microscopy data:

3D Doctor

3D Doctor has been on the market for a long time. It allows reconstructions from MRI, CT, PET, and microscopy. It lets you export polygon models to formats such as .obj, .dxf, .3ds.


OsiriX is another program for 3D reconstruction of non microscopic scale objects and can work with MRI, PET and CT.

Animation Software Specific to Medical Animation

As i said before, medical animators commonly use general 3d animation software to create their work.  Medical 3d reconstruction software is often used to bring in real life data into the animations.  There are other programs which are specifically created to help with medical and scientific animation.

Software programs for opening Protein Data Bank structures allow you to visualize them in different forms and import them into your animation programs or animate as is natively.


Chimera is a program for the 3d visualization of molecules which are commonly used in medical 3d animations.  It has various molecule model display types such as ball and stick, ribbon and surface and allows you to morph from one structure to another to show conformation changes. Chimera has some basic animation capabilities such as fly-through.

Visual Molecular Dynamics

VMD allows you to visualize and animate biomolecular systems even over 100,000 atoms.  It can open Protein Data Bank files.


Pymol is a molecular visualization with an assortment of display types  and scripting.

Molecular Maya

Molecular Maya is a plugin for Maya which allows you to import molecular structures, visualize and animate them.  It customizes Maya to work with molecules and the Protein Data Bank.  It includes a rigging kit to rig molecular models as if they were characters.  It also includes a double stranded DNA kit that automates modeling and animation of DNA.  Additionally it has a cytoskeleton kit that helps with accurate modeling of microtubules.


As you can see, the question of what the best software for medical 3d animation is is not a simple one.  There are tools specific to medical animation as well as software built for general animation that you can use.  Some software packages have well developed animation, modeling, rigging and dynamics modules while others lack some completely.

It is not an easy choice to make.  If you already have experience with a package or two you may have the upper hand.

Having tested various packages, I would say once you get past the learning curve, Maya is a good choice for medical animation.  3DS Max comes in second and Cinema 4D third.  I would also pick Maya if you work for yourself and need to get everything done in one package.  Of course, if you work for a company, the choice of software may be dictated to you.

You always have the option to test drive a software package and follow some tutorials to make a few animations and check out the toolsets.  Animators have their own preferences in how they work.  You will be spending a lot of time working in the software so it needs to fit you well.  For example, Maya has extensive menus that can be brought up anywhere your mouse is on the screen which makes work faster.

Lastly, you are not married to any one tool.  Animation workflows allow you to use various programs for different parts of the pipeline.  Just make sure you know the limitations when it comes to moving your assets between programs.  You dont want to spend days texturing an object and then find out your animation package will not accept it.

I hope this article has helped you in choosing the software you need.  Click the following link to learn if you can teach yourself 3d animation.

Dr. J

Dr. J has worked in biology all his life and holds several advanced degrees and certificates in biology, anatomy, scientific illustration, 3d animation and motion graphics. He has always had an interest in teaching others the wonders of biology using the latest advances in graphics, including visualization, digital microscopy, animation, illustration, VR and interactive media.

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