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Amy Sterling

Ideas to improve ruinous mess of meshes?

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Hi there!

 

I'm new to C4D and working on animations for our neuroscience lab. Today am trying to visualize potentiation, the strengthening of synapses (connections between neurons) in the brain. We have reconstructed thousands of neurons at nanoscale resolution from electron microscope images, so the model neuron I am using is a real cell and I'd like to show some of the spines, the projections sticking out, grow and shrink in size.  This is only half of the synapse - they would be connected to another branch that also thickens, but I haven't gotten that far yet.  I've managed this using Bulge

 

349889517_potentiationlowres.gif.430de8de8dc72d0067799bec3e105adc.gif

 

but it deforms the stem pretty badly. Here's the project file where I tried also Subdivision Surface and Squash & Stretch, but neither really worked prob because I'm doing it wrong. Any ideas for a better way to do this? 

 

In the brain, these blobby things get larger with use and smaller/eventually shrink away when they are not used, which is how learning is represented. Here is an example animation showing the other half of the synapse that will at some point be added once I figure out how to make them get bigger/smaller :) https://youtu.be/xJIacDRaCKw?t=12

 

 

Thanks for your time!

Amy

 

 

 

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Generally speaking things deform badly when the topology is not good enough to support that deformation. And that is indeed the case with your model, which is, I'm afraid to say, a ruinous mess of triangles lacking either the uniformity, density or polygon integrity required to deform well.

 

The best you can hope for is to select the polys in the relevant part and try and subdivide that a bit further and hope you can get enough resolution to the triangles that their triangular form is no longer apparent in the deformation. Look for the subdivide tool in the right-click menu. Don't forget to tick the smooth button. 

 

Another way to rescue it might be the Volume Builder in R20. Though with a model that complex you will need quite some serious computing power to be able to usefully work with it...

 

CBR

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  • Yeah unfortunately exporting .objs is sort of a hack, and a bad one at that. A ruinous mesh of triangles indeed ha. I imported the raw file into Meshlab and used quadratic edge decimation to reduce the face count by ~50% (it's 1.5M on the full model, and this model is about 1/50th of a whole neuron) so that may be contributing to the low density. But yeah generally the meshes are sh**. I will make a separate thread posting a raw .obj and asking if anyone has ideas as to how I could improve it.

     

    I'll give the Subdivide and Smooth options a go. Thank you!

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    I have an idea how you could improve it. Try running the hi-res original through a little application you can find called Instant meshes. This will retopologize it as quads, and allow you set a detail level and do poly reduction without compromising that. Very useful little tool that one...

     

    https://github.com/wjakob/instant-meshes

     

    You need the pre-compiled binary for your OS, so scroll down the page until you see those...

    Also don't skip the manual / overview ! It's a 2-click procedure, but you need to know what those 2 clicks are ;)

     

    CBR

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  • Thanks! Ok we got this running and played around with exports but it is majorly deforming many of the spines. See how they have become hairlike thin tendrils? Some of them are even severed entirely. This mesh is with 10 smoothing steps and it still looks low-poly. When I try to save a smoothed version out of meshlab, the program freezes entirely.

     

    here are the mesh files in case you have any other ideas.

    Instant Mesh Mesh

    original resolution mesh

     

    image.thumb.png.750fa04b756d80b8b8ac06b1d8598acc.png

    image.thumb.png.a842d10bdafcff7afc36af758cf9a472.png

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    These files are horribly large and are strange (open in C4D).. I think your objective would be better served by a simpler model to illustrate potentiation. Perhaps a model synapse attached to the 'tree' that would be easier to animate with a spline where scaling the synapse would be more straightforward. You could use mograph to elaborate.

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  • 845118669_cortexneurongold.thumb.png.e82782ee1531639d05cf6610df43ca5b.png

     

    Hi there, 

     

    I'm learning C4D to make animations of neuron meshes from our lab. Unfortunately it has come to my attention that our meshes are utter sh**. 

     

    Here is a raw mesh

     

    Steps I've tried to improve them:

    - quadratic decimation in meshlab

    - smoothing in meshlab

    - Instant Meshes

     

    Any thoughts? 

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    Again, the actual model is too large for what you want (to illustrate potentiation?). Model a synapse (with a spline to enable animation) and use mograph to sprinkle them around  on a simple neuron. I understand your desire to animate the real thing but, even then you would need something smaller to reach a manageable size. 

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    That is a mesh with not enough resolution to describe the thinnest parts of the form. If you must attempt to animate the whole mesh, I'd try again in IM, but with higher target polycount.

     

    But I agree with Anthony above - you'd be mad to try and animate this whole thing directly. His idea is the best way forward I can see - make a nice, all-quads detailed model of a synapse, its animation driven by splines or deformers, and use the cloner to distribute them over the main model.

     

    CBR

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    Do you have the chance to work with Zbrush? The autoretopo functions it has are the most Advanced out there. Doing it manually would be a nightmare with complex irregular forms like this.

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    Basically, there are far too many polygons to deal with. Whatever you do, eliminate most of the file so that you can illustrate potentiation with something of reasonable size.

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