Working with photogrammetry, laser scanning, and all the other techniques I dabble with/intimately rely on, I generate a lot of 3D data. For the most part that data is usually very high resolution, and often quite noisy and in need of cleaning up. I want to detail here some of the software I’ve come across that can be used to clean up, reduce, and generally process 3D data – particularly meshes but also point clouds. As usual, my focus is on freely available software.
If I produce a high resolution mesh with photogrammetry, say, then here’s what I’ll generally want to do to that data:
- Clean it up – remove spurious parts of the mesh
- Merge meshes – If I’ve had to scan an object in two attempts (top and bottom), I’ll need to align those meshes ideally algorithmically, but by hand if I have to.
- Reduce the mesh – reducing the number of polygons makes it easier to hand the mesh for rendering etc. I’ll often keep the high-res mesh for measurements, and a lower res mesh for visualization.
- Retopologize the mesh – this is something I’ve only recently got into, but essentially retopologizing the mesh makes the polygons more evenly distributed. For most of my purposes, this isn’t entirely necessary, but for animation/modelling and the like, I gather it’s good practice
- Re-texture/generate UV maps – I hate working with textures. Photogrammetry will generally produce a model and a texture file. But once you start editing your model, you may wish to re-texture it. Depending on your work flow, that may mean regenerating the UV maps (which tell software where to put which parts of the texture on your model) and for high-resolution meshes this is not a trivial task.
As I list the software, I’ll include the above tags to let you know what it can do.
Autodesk MeshMixer [clean][reduce][retopo]
Link: http://www.meshmixer.com/
Meshmixer is a phenomenal piece of free software. It’s really designed for preparing models for 3D printing, but it’s tools for generally cleaning up meshes are fast and easy to use.
It loads data very quickly, and has a pretty wide range of tools for editing meshes, including sculpting brushes, tools for reducing and retopologizing meshes, and analysis tools for fixing holes/intersecting polygons and so forth.
Autodesk Meshmixer has become my go-to software for general mesh maintenance.
Meshlab [clean][merge][reduce][retopo][texturing]
Link to official site: http://www.meshlab.net/
Meshlab was a staple of mine even during my PhD 10+ years ago. I was going to start this section by lamenting that it hasn’t been updated in years, but having just visited the site I see that a new version was released literally just a few weeks ago, version 2020.02.
It still looks and does almost exactly the same as it has for the past decade, which is to say it does a lot. The menus are expansive, and contain almost everything you could want for cleaning up meshes and re-texturing.
The biggest drawbacks, in my opinion are that there’s too much to chose from, and historically it’s been a bit… crashy, when dealing with big meshes. However, the former point is much alleviated by the relatively new addition of the search bar in the top right, which enables you to find functions much faster than digging through the menus. It remains to be seen if the new version is more stable than it used to be, but here’s hoping.
CloudCompare [clean][merge][reduce][retopo]
Link: http://cloudcompare.org/
CloudCompare really took over from meshlab a few years ago for me – it has a toolset more in line with the tasks I tend to do, and is just a bit easier to use. As the name suggests, it was developed originally to work with point clouds, and one of the nuances of using cloud compare is that some functions need to be applied to the vertices of a mesh, not the mesh itself.
My favourite use of CloudCompare is to align two meshes. It uses a rough and then fine alignment tool to get things really nicely aligned and then merged.
It’s generally pretty quick, but can struggle rendering larger meshes, even the Phalange in the screenshots above caused some stuttering when viewing the mesh.
Instant Meshes [reduce][retopo]
Link: https://github.com/wjakob/instant-meshes
Instant meshes is fantastic at one thing – reducing the number of polygons in a mesh. It is exceptionally fast at doing so:
Two downsides: firstly, anything you decimate in this way will need UV mapping, and all texture information will be lost. You can use something like Meshlab to generate UVs and then either Meshlab or xNormal to transfer the maps between meshes.
Secondly, when you save the file, you have to type the file extension for obj or ply. This is a minor point, but it catches me out Every. Single. Time.
xNormal [texture transfer]
Link: https://xnormal.net/
xNormal is used for transferring (among other things) texture maps and normal maps from high poly meshes to low poly meshes. The former, texture maps, means colour is transferred over, while the latter, normal maps, means that even though your new mesh is low poly, a lot of the fine detail is preserved. However, xNormal does not UV-map for you – so you have to do that first in Meshlab, or Maya or Blender, or whatever unwrapping workflow you use.
This whole task is far more niche, at least for dealing with 3D data in my usual capacity, but I include it here because it deserves a mention.
To show you what these do, I’ve rendered some images with Maya:
Clearly, decimating the mesh and normal mapping it isn’t losing appreciable detail, but vastly reduces file size, making it easier to work with. Of course, as outlined in two recent papers here and here, you should always keep the raw data (in the case of photogrammetry, the photos), so that high resolution models can be used or at least remade in the future as necessary. But, it may make sense for your own purposes to downsample and re-texture just to make working with the models easier.
Summary
Those are the pieces of software I regularly use for playing with 3D data. I’m sure there’s more, and I’d love to check those out if I haven’t already, if you leave suggestions in the comments.
Similarly, if there’s demand for a more detailed workflow for any of the processes I’ve touched on, I’m happy to put together future posts to cover that.
[edit] – I’ve deliberately not included Blender (completely free) or Maya (free for educational use) because those are monster programs for far more than what I’m talking about here. They also tend not to be as good at some of the functions above, particularly around mesh decimation and retopology, when working with very large meshes. But, I still find myself using Maya frequently for some of these tasks, and it’s new remesh and retopologize functions in v2020 are pretty good.
Dr Peter L. Falkingham 
Hi Peter,
I would certainly be interested in seeing a workflow for Autodesk Meshmixer if you have time!
Thanks,
Jim
Dear Peter,
I optimize and retopologize the 3D models with Blender 2.8, and works very good. Maybe Instant meshes improves the retopology or at least it is easier to use.
All the best,
Ina
I find that blender isnt particularly quick with big meshes. Instant meshes is orders of magnitude quicker and more stable. But yes, Maya and Blender can both do all these tasks to some extent.
Nice list for editing mesh. I use Zbrush Zremesher, Xnormal, Maya quad draw tool and sometimes I use Topogun for faster workflow.