Anatomy and Art

a blog by Sara Egner

Archive for the ‘C4D’ tag

Neurons

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So I recently learned about some very cool things.  First off, there is a site out there that catalogs neurons  http://neuromorpho.org/  It’s great, you can browse them by brain region, by species, by cell type, and pull up and view a vast assortment of known neurons.  So that’s pretty awesome on it’s own.  But I was lucky enough to learn about this site in connection with the work of Nick Woolridge, who has been writing code to make the data found there importable into Cinema 4D or ZBrush.  This is his video on Vimeo explaining the process of using this data in Cinema 4D and where to find his script.

Using the NeuronBuild C4D script from Biomedical Communications on Vimeo.

Some of the larger neurons can bog down the computer, but I had good luck trying it myself, and I’m really excited about having this available.

neuron import into C4D

Written by Sara

March 28th, 2017 at 11:46 am

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C4D Live Tutorials Airing Presently

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I am a fool not to have mentioned it before, but the NAB is offering some great tutorials online right now.  There is a fantastic one airing right this moment about mograph and dynamics in medical animation by Thomas Brown.  Do check out http://www.c4dlive.com/ if you get a chance today, or through Thursday.

Written by Sara

April 8th, 2014 at 3:09 pm

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Showing Exponential Growth in Bacteria

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So I got an interesting request from the math department at Sapling Learning about a week ago.  We wanted to show the concept of exponential growth, using bacteria as the example.  So one bacterium divides into two and they each divide into two and so on.  We decided to take this through six generations landing us with 64 bacteria on screen by the end of it.

So the catch was, how to move 64 bacteria around as one, and then as two with an equal number of divisions nested inside and then as 4, each with an equal number of divisions inside, and then as 8 and so on.  So I got a little complicated with my object hierarchy for this one.

screenshot object hierarchy

So I had one called cp_start, short for clostridium perfringens (a bacterium capable of reproducing at the 15 minute generation cycle that we wanted for the example) with a bend object on it.  And then nested within that one was a duplicate called cp_15, another called cp_30, cp_45, cp_60, cp_115, and cp130, to represent the ones that would branch divide off at the 15 minute, 30 minute, 45 minute, hour, hour 15, and hour thirty points from that one, all with their own bend objects.  Then within each of those I had further duplicates that would still occur from each of those.  Within cp_45 there was cp_60, cp_115, and cp_130, but cp_60 would only have cp_115 and cp_130.  And then so on with each bacterium.

In the end it worked out, and the extra arranging effort was well worth it as the sprawl pattern of bacteria had to be adjusted after the first time.  My first attempt had them all more compactly arranged, but one of our biology experts explained that bacteria could only continue a regular exponential growth cycle if they were able to get to more food.  If I hadn’t had them nested like this, it would have been incredibly hard to go back and make them disperse further.

bacterialgrowthprogression

I added the timer and count in After Effects.  The whole thing plays at a sped up pace, showing one minute per second of animation.  And I think it looks good.  I hope that we get to use it for biology content someday as well as for the math example now.

Written by Sara

September 30th, 2013 at 10:32 pm

DNA Replication – 3D Animation

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Hello again readers!  I’m so happy to be able to finally share with you all an animation that I worked on some months back for Sapling Learning.  Some of you will recall me writing about this one before.

The 3D models were created by studying the molecular sizes and shapes of the relevant molecules and then creating simplified representations. The 3D animation itself was created using Maxon’s Cinema 4D. Then the individual shots were composited together in Adobe’s After Effects. Audacity was used to record the narration, and then it was all put together for timing in Final Cut Pro (I still use an older version and cannot speak to all the changes they made in X.) I went back into After Effects for further labeling and effects (like the zoom into DNA polymerase) after that. So that’s the basic work flow.

There are a lot of biochemical processes that feel like a very complicated ballet as you get further into them.  Putting together the action of everything happening at the same time for the final shot in this animation really got me thinking about that analogy again.  And the truth is, that when this actually happens in nature, that lagging strand is actually being whipped around by helicase and read in an even more complicated fashion.  I really like that we emphasized that we were simplifying for clarity with this one.  A lot of educational materials would just let students find that out later if they went on to the next step in their studies.  That kind of thing always bothered me when I learned about such processes in school, and I’m happy to be with content experts who are willing to take the time to either make something more accurate, or let students know when things are being brushed over or left out of the picture for clarity.  I think that kind of thing is important.

Anyway, I’m really happy to be able to share this with you all.

Written by Sara

April 7th, 2013 at 9:03 pm

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Animating DNA

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I’ve been doing some work to get started on a new animation at work lately.  This one is about DNA replication, and some of the animation needed to tell the story is making for some interesting challenges.  Now, if you just want to model some DNA within Cinema 4D, this is hands down, the best tutorial I have seen for that.

http://www.bmc.med.utoronto.ca/bmcwiki/doku.php/technologies:cinema_4d_tutorial_-_schematic_dna_1

There’s a part 2 to that too, so do keep going if you get into the first one.

The trouble with this model though, is that you can’t unzip the DNA to show how replication works.  So I’ve been trying some alternate methods lately.  At first, I was very excited about getting the backbones to open up like this.

But I still couldn’t get the bases to work with me.  That version was utilizing the helix shaped splines and sweep nurbs set at 130º.  And the spherify deformer could be animated to open the double helix according to keyframes.

One of the tricks with trying to do this is that you can’t apply your deformers to the double helix at large without mangling your model.  You do a lot better to apply them directly to your splines and set up your bases as cloners to those splines, and your backbone as sweep nurbs along those same splines, so that the individual strands maintain their shape.

I also learned, that it’s much easier to line up your bases if you start with a straight ladder sort of arrangement, and then apply twist deformers to a null object containing the double helix so that they stay together.  You can then animate your deformers along the strand to wind and unwind your DNA, and with the addition of an FFD deformer along each spline, you can then animate the stream opening as you unwind it.  And the big trick, that you might not think of with that – uncheck the align clone option in your cloner.  For hours and hours, everything I did sent my bases all over the place, until I finally tried unchecking that box, and then they stayed align.  I could go on about that for a while, but the important thing is to mention it so we all know not to get stuck like that in the future.  Honestly, now that I’m thinking about it, some of my earlier attempts may have actually worked out, had I tried unchecking that box sooner.

And of course, being a big crazy 3D program, there are absolutely other ways of getting at a solution.  In looking for ideas with this one, I wound up using the AMI listserve’s professional groups, and came across an animator in Germany named Andrej Piatkowski who found a way to do this without using splines at all.  He felt like they just got in the way, and as you can see, he got some really cool results with what he did.

He doesn’t have it connected on the other side, the way I’m wanting for my purposes, but I love how neatly everything fits together and then rips apart so smoothly.

So remember, in your own efforts, there are many paths to the solutions you seek.  But hopefully something here can help you out a little if you’re doing similar work.

Written by Sara

December 2nd, 2012 at 8:23 pm

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Translation – The narrated version is up and public

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http://youtu.be/yxEhmD6cNyg

Last week I got permission at Sapling to post the new animation. I went with the narrated version for now. I may post the silent one at a later date.

I learned a lot putting this together. I learned a good bit about working with cloners in Cinema 4D, and got to practice with C4D’s shaders, and even touched on coding a bit with trying to get that mRNA strand to move the way I wanted it to.

All in all, I think it came out really well, both versions actually. I’m proud of it. And I’m really enjoying working with such amazing and knowledgeable folks over at Sapling. I learn the coolest stuff from them, all the time.

Written by Sara

August 28th, 2012 at 9:12 pm

Animation in Layers

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Goodness me, it’s the 4th of July and I intend to go jump in a pool and play in a little while.  But first I wanted to pop in and say a few words over here.  Lately over at Sapling I’ve been pretty consumed with an animation that I’m putting together over there.  It’s been a whole lot of work, and it’s nearly finished now.  I get excited at times like these.

The animation is about the translation process.  From a technical standpoint, it’s been interesting how much time I’ve been spending in the program, After Effects.  I usually do a little compositing there, but then have generally brought my work into Final Cut Pro or something like that to finish up the actual shot arrangement.  With this one, I’ve found it made more sense to actually just put the whole thing together in After Effects.  I’m having to be really careful about organization and use a lot of pre-compositions. And even so, I don’t believe that I have ever taken on this many layers of video to wrangle for another project in my entire life.  That’s the thing about animation though I guess.  You literally make all of it from scratch.

One thing that I don’t care for in After Effects as opposed to your more editing and less effect driven software, is it’s insistence that every little thing have it’s own layer.  This has been one of those pieces for which I’ve wanted a lot of layered subtlety going on behind the scene.  It would have been nice to be able to dedicate a couple of tracks for that, rather than adding a new one for every piece of footage used.  That being said though, After Effects does a great job at handling image sequence footage and you do have a great deal of control over a lot of details.  Still, if anyone from Adobe happens to read this, maybe the next version could at least give us the ability to group tracks into folders.  For when you don’t quite want to create a pre-composition and send your tracks to another timeline, but you still want to clean them up a bit for viewing sake, or to add some sort of matting to the whole bundle, just that one little thing would make After Effects so much better in general.

I especially thought that when I got into the part of this animation that I like to call the breakdown.  Textbooks often use similar static illustrations to represent things that may or may not atomically look like the molecule in question.  And really it’s only rather recently with the work of Dr. Venki Ramakrishnan (video link to a  lecture of his about the ribosome and translation process) that we even fully know the exact structure of the ribosome.  So one of the things that I’ve been excited to do with this one is to create some more standard looking images and then layer them over the 3D animation.  I then keyframed the individual components to follow their 3D counterparts so we can actually see the connection between those representations and a more 3D space.  I have been simultaneously irritated with myself for coming up with such a time consuming and intricate thing to create to tell this story, while also really psyched to get to break everything down so clearly.  As it’s come together, every codon in the 2D overlay has had to have it’s own layer in After Effects, but now that I finally have everything placed and animated, I’m really excited about it.  Back in school, I recall one of our teachers, John Daugherty, telling us about how every piece that you do has to have that thing that makes it really interesting to you as an artist.  Whether it’s a concept, or a technique, or whatever, and I think this part of this animation is that for me.  It’s something that I don’t see other animations doing, and for me it’s like wrapping up that little aha moment that you get when you’re watching these sorts of things and you finally figure out how one representation relates to another and start to get what it is that you’re seeing.

As you can see, though, I’ve got these huge blocks of layers in the timeline there.  At one point, I had more than 60 in there, and that’s with many of them being pre-compositions that lead to more layers in another timeline.  But it’s working.  And I just love it when things work.

This is going to be a good one.

Written by Sara

July 4th, 2012 at 1:20 pm

The Enzyme Substrate Complex

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So, some of you may remember my recent post, “Molecules Molecules Molecules.”  Well I’m really psyched to be able to share the animation that inspired that post with you all online now.

 

Enzyme Substrate Complex from sara egner on Vimeo.

I’m excited to get to show a little bit of the kind of work I’ve been doing lately over at Sapling. And I’m glad I get to share this one in particular because I know it goes just that extra step beyond the kinds of videos you find on this subject out there. And I’m loving that we get to make things like that. I get to work with biology experts. And when things get really really tiny, no one says, well that’s really just chemistry at that point – don’t worry about it. We just talk to a chemist about it. And if I hit a technological glitch, we have those kinds of experts around too. And I’d thought that my move into grad school was going to be a move away from all the video work I used to do. But here I am drawing back on all of that experience to make things like this now. And of course my whole little fascination with ATP comes in to play with this one. But that would be a whole other story. And this writer is winding down for the night.

Written by Sara

May 8th, 2012 at 10:12 pm

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Bugs!

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So, I’ve been doing a lot of work in Cinema 4D at the new job lately (with Sapling Learning), and most recently that’s been getting to make bugs and make them fly.  Basically we’re animating a classic genetics example with different colored bugs, and what this has meant for me is that I’ve been able to make one of the more complex models I’ve done to date with this program in making my little bug to begin with, and then I’ve also been able to get into joints and IK rigging with the program.  This was something I’d done once before in 3DsMax, but not really had a lot of experience with.  The main thing I wanted the joints for was the flapping of his wings, but by giving him a spine I was able to turn his head and body a little as well and the little guy that much more life.

I had some difficulty for a while with getting the joints to work correctly.  I wasn’t able to use any of the templates, so in the end I just used the joint tool and ctrl-clicked my way through the construction of wings.  You then go through and place the IK chains which will define how your object moves as a whole.  Cinema 4D will automatically assign your object a skin tag which will allow you to get more natural looking movements.  To set up the wings I used a linked symmetry in modeling the joints.  It was great for modeling, and for recording the keyframed animation of the wings flapping, but that later proved problematic when I tried to move my bug around the scene.

What you’re seeing there is my poor little bug’s right wing being pulled off as he moves away from the Z axis in an attempt to keep that linked symmetry across that axis.  Naturally I was convinced that I’d made a huge mistake and there was no getting out of it without undoing at least a day’s work.  But it wasn’t the case.  As it turns out, when you select the individual joints themselves that are doing the mirrored symmetry, you find a tab that allows you to adjust that symmetry.  And because my model had a spine, I was able to change the symmetry from world to object and select a joint in the spine as that object.  So I didn’t loose my joint structure, or even my keyframing of the flapping.

Being free to roam a 3D world again, I was able to make copies of my bugs and draw splines for them to fly along.  In the end it all looks and feels a little like designing a roller coaster.

It’s strange, modeling in so many layers.  Conceptually I sometimes have difficulty getting my head around moving the skeleton and taking the bug with it, vs moving the geometry, or the hypernurb or skin itself.   It’s easy to get confused (well, it is for me anyways).  But I have to say that I think there is something to all these rumors of Cinema 4D being more intuitive than other competing programs.  Sometimes things just work.

Oh, and one last note for all the rookies out there like me…  My art director suggested a couple changes, one of which was giving my bugs some eyes when she saw what I had going.  So I did, but had a little trouble with them falling right back out of my bug’s head when they would fly.  There was no binding or boolean that was quite going to get me around this.  But having that spine in place saved me again.  I made the eyes a child of the last joint that controlled the head’s movement and that did the trick perfectly.

I’m pretty well on to After Effects with it all at this point (time to make it pretty, and also bring the focus back to making it a clear and understandable example of the principles it was created to display in the first place), but I just wanted to get a few notes down here as to process and getting unstuck as problems come up.  I’m finding that whether or not any of you readers are using this blog to work your way out of tricky spots in animating, I seem to be coming back to it to remind myself of things more and more.

Written by Sara

March 31st, 2012 at 2:05 pm

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Animation and 3D capture software

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So, last Friday, I had a little time in the morning to watch a tutorial.  My co-worker, Alex, had recommended this one, and she was right.  For those of you learning Cinema 4D like I am, this tutorial not only gets into UVW painting and pelt mapping, but is also a really great modeling tutorial.

 

So, I’m telling her how great this is, and she tells me that Greyscale Gorilla (the company that puts these out) is appearing that very night at a Cinema 4D/ live music event (SXSW, really brings all kinds of events out of the woodwork here in Austin.)

So I went, and it was a really good event. When I got there, a man named Nick (and unfortunately I can’t remember his last name) taught us a bit about using Cinema 4D’s cloner and animating spheres along a spline. I definitely learned a few things from that talk. And then the next speaker was a man named David Lewandowski who spoke about his use of Cinema 4D in a new music video. His talk was fun because it was the first time I’d seen anyone integrating this stuff into actual video to do special effects. And what really caught my attention was the 3D scanning software he was using to capture the actors’ faces into his 3D software and integrate it within the video.

Back when I was training with the craniofacial clinic at UIC, there was a lot of attention to 3DMD and working with CT and MRI data to get 3D data for both surgical planning and also facial prosthetic development. I have spoken with various anaplastologists over the last few years about this as well. So when this guy gets up and talks about how he pulled together this video on a shoestring budget and paid about $50 for some Russian software that he used to upload photos of the actors (all taken from the same camera), and got these seemingly accurate 3D models out of them, I had to ask him about it later.

He told me that the software was called Agisoft Photoscan, and that there is also an Autodesk product currently in beta testing called Photofly. The friend I brought with me to the event told me that some people are even hacking into their XBox 360 gaming consoles and managing to capture 3D data through the technology already present in those machines as well. I find all of this to be very exciting from the perspective of what potential it brings to a field like anaplastology where you have a strong need for accurate 3D information about patients, but not always the financial structure to afford the latest and greatest technology at every turn. This also opens the door to better international consultation. If all one needs on the spot is a decent camera and an internet connection, then better information can be sent overseas allowing for better preparation before a patient makes the trip in person. Possibly, you could even come up with a good temporary piece for someone to wear in the interim while they are waiting on their final prosthesis to be made.

I leave you with this short YouTube clip of someone playing with Agisoft’s software to capture movement.

And I’d better get going because there is another one of these little 3D get together’s tonight!

Written by Sara

March 13th, 2012 at 8:36 pm

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