Anatomy and Art

a blog by Sara Egner

Archive for the ‘animation’ tag

The Wiggle Expression

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Recently at work, I’ve had cause to use the wiggle expression in After Effects.  If you’ve never done this, it’s pretty simple to set up.  First, open up the transform controls in your timeline for the object to which you intend to apply the effect.  Then alt-click the position stopwatch.  You’ll be prompted to add an expression in the timeline under the layer, and there you’ll write wiggle(1,20).  Actually, the numbers will be whatever you want them to be.  The first specifies how many wiggles per second you want to apply.  The second specifies the amplitude of the wiggle in pixels.

In my case, this effect was really great for bobbing around a bunch of molecules in a scene.  But I ran into trouble when I wanted to ease up the effect for more control.  To use my example again, I needed molecules to bob around in liquid, and then pass through a semi-permeable membrane, which required more control over them, and then go back to bobbing about.

screen shot of water molecules moving across a semi-permeable membrane

So, to do this, you need a slider control layer.  So you’ll create a new adjustment layer.  Then under the effects pull-down, up top, go to expression controls, and then slider control.  Then you’ll highlight the number on your expression that you’d like slider control over.  In my case it was the amplitude (see the 20 in the example).  With that number highlighted, you’ll grab the pickwick (looks like a swirl) and literally pull it up toward the slider stopwatch.  You’ll see your code change it it’s worked.

Your wiggle expression will then be defaulted to zero until you dial the slider control up.  Now you can keyframe that feature to begin slowly, or to reduce mid animation for greater position control when you need it.

Some of this is easier to understand when you see it, and doesn’t really lend itself well to explanatory screen shots.  This YouTube video by Ian Killick does a great job of showing the process…

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September 30th, 2017 at 10:19 am

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DNA Cloning Animation

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I recently had the pleasure of working on an animation to teach students about DNA cloning.  This is one of those exciting ones where I feel like we really added to what’s out there on this topic.  So naturally I wanted to share it here as well.

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June 11th, 2015 at 9:25 pm

Rodin’s Hands at Stanford

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There is a really interesting exhibit happening at the Cantor Arts Center at Stanford.  I believe it opened just yesterday, and will be there until August 3rd.  It’s called Inisde Rodin’s Hands: Art Technology and Surgery.  You can read Stanford’s coverage of it directly here.  Or you can watch this video with James Chang speaking a bit about noticing specific physical maladies in Rodin’s sculptures when he was an undergraduate, and how this project grew from that observation.  Now he incorporates the study of these sculptures into his hand surgery educational program where students diagnose and correct the maladies observed.

 

Sarah Hegmann, who I went to school with, put together this animation bringing Rodin’s hands to life as part of the exhibit.

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April 10th, 2014 at 8:24 pm

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I Will Learn Premiere

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Today I am making a commitment to make this the year that I finally learn to really use Premiere.  I have had it with pushing After Effects to do longer animations than it is geared for, and it’s long past time to get over my old version of Final Cut Pro falling further and further behind the times, and the new versions are not going to redeem themselves.  The truth is, Premiere and After Effects have been crafted to work seamlessly with one another.  I just have to take the time to learn those tricks.  I’m about to have a Lynda.com subscription again, and I am making this a high priority goal.  Premiere has gotten really good in recent years and I know that I’ll like it more as I learn more of the same shortcuts I had in Final Cut Pro.  It’s not like I haven’t used it at all.  I just get angry with it for not being the Final Cut Pro I used daily for so much of my life.  Now I can use this one instead.  It’s time to get over this meager hurdle already.

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January 30th, 2014 at 11:30 pm

Area and Volume of a Cube

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Just a nice little math visualization that I made in Cinema4D and recently posted to YouTube

 

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November 22nd, 2013 at 8:36 pm

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Rocky

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I started to post something tonight, but had a moment of doubt about my terminology.  So instead, I’m now deleting that and taking a personal moment to show off my awesome new dog named Rocky.

 

Rocky

He’s a shelter rescue mutt, part welsh corgi and part pit bull they say.  If you’ve ever doubted the significance of genetics, just look at dogs.  They come in such a variety of sizes and shapes, and good portion of those moves have been intentional on the part of humans.  It’s a weird deal.  But I sure am glad to meet this guy.

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November 18th, 2013 at 11:16 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.

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April 7th, 2013 at 9:03 pm

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To This Day – Spoken Word and Animation

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Wow. This is more about humanity than anatomy, but it is absolutely art. I saw this online tonight and wanted to share it.

I wasn’t familiar with Shane Koyczan prior to tonight, but it would seem that he is a spoken word poet who got his start in Vancouver.

You can learn more about him, and “To This Day” at his website here http://www.shanekoyczan.com/

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February 22nd, 2013 at 1:19 am

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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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