Anatomy and Art

a blog by Sara Egner

Archive for the ‘3D’ tag

3D Printable Periodic Table of the Elements

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I’ve been working on a little side project lately at work.  For a long time now, I’ve wanted to get into making 3D printable educational materials.  Our focus on accessibility of late may allow me to do just that.  Did you know that you can download a font for braille, just like any other font?  So I’ve been playing around with a braille version of the periodic table of the elements.  Obviously, this does no good in a web image, but when incorporated into a 3D printable file, suddenly useful.

image of 3D printable periodic table

I haven’t had the opportunity to test this with a printer yet, but I’m working toward that.  Once I have that, I can make adjustments to the digital file and perfect it from there.

I think that if I can optimize this for use, and if schools actually download and print them, that this could be a great addition to our educational offerings.  Really, I’m surprised that I don’t see more of this kind of tool around already.  I really think that we will in the years to come.

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July 20th, 2016 at 1:58 pm

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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.

Written by Sara

June 11th, 2015 at 9:25 pm

Update

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Well, while things may not look any different, welcome to the newly hosted AnatomyAndArt.com!  With Speedy Puppy closing it’s doors in a couple of months, I’ve been making the transition over to A Small Orange, a web hosting company run right here in Austin.  So far, everything seems to be working.  So yay!

A lot has happened since my last post here.  Since my last post here, my mother was diagnosed with cancer.  That’s been huge, and just a real crash course in cancer treatments, ER failings,  ICU care, neurosurgery, and all of that.  I suppose I haven’t really had it in me to write about all that.

I also gave that talk to the 8th graders for career day.  And that was so worth doing, both for the reflection it gives you on one’s own path, but also for the connection you make with the up and coming generation.  If anyone ever asks you to do this, I have to recommend going for it.

The holidays have also come and gone.  I actually had a cute little Xmas card this year, created in 3D that I’d intended to share here.  I suppose I could go ahead and do that now belatedly.  Rocky and I do wish you all love and warmth for the holiday season, and future seasons as I’m not getting this up until January.

Christmas Wreath 2014

I also finished another painting.  I think it has a buyer in California already. And I started another one too.  So it’s been a very paint heavy beginning to the New Year.  And then just last night I met up with some fellow artists in Austin and we discussed potentially building a show to take our work into a couple of cities.  I’m loving the idea, and really hoping that it comes to fruition.

And so I suppose I’ll leave you with an image of the latest painting, and return with images on the one in progress as it gets further along.  Introducing Tree #8

Tree #8

 

Written by Sara

January 19th, 2015 at 4:04 pm

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3D Printed Anatomy

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Monash University in Australia is releasing their new 3D printed anatomy series.  The press release is here… http://www.monash.edu.au/news/show/3d-printed-anatomy-to-mark-a-new-era-for-medical-training

And if you can access the full article, more details about it are published here…
http://onlinelibrary.wiley.com/doi/10.1002/ase.1475/abstract

And I first heard about it through Meddeviceonline’s article which contains the following photo.  If that is an actual comparison of cadaver and the plastic version being made by Monash, well that’s really impressive…
http://www.meddeviceonline.com/doc/world-s-first-d-printed-cadaver-could-revolutionize-medical-education-0001

cadaver

Most of these articles talk about the value of having these models as a replacement for human dissection all together in classes.  I don’t think that a complete replacement will ever be a good idea, certainly not anytime soon.  But a really accurate model like this, could be incredibly valuable used in addition to cadaver studies.  Which leaves me wondering exactly how they’re getting it.

The abstract of the scholarly article mentions injecting contrast into specific anatomy to highlight it for the scans.  That would certainly help, but I’ve seen enough CT data to know that it’s going to come out with a lot of mess too.  Whoever is going through and isolating this piece from that and isolating the model is doing a fine job of it.  That’s for sure.

I’ve had a bit of  fascination for the last couple of years with the idea of making educational models that can be printed out in 3D on the user’s part.  This is definitely more complicated than that, and they are not suggesting that students try to print their own.  But I feel like that’s around the corner.  And it’s exciting.

 

Written by Sara

July 17th, 2014 at 8:49 pm

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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

3D from 2D

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My plan to get a full figure out of 123d Catch has so far fallen flat.  My efforts seem to alternate between mostly outright failures sprinkled with unusable results.

Screen Shot 2013-09-04 at 11.30.31 AM

I think that the best capture we got was in the office lunch room, using the iPad.  As you can see, we still got a lot of scatter from the surrounding room.  And it’s harder to see in this image, but you can tell that there was a tiny bit of movement that resulted in a little bit of distortion in my model, Ernest’s, face.

Screen Shot 2013-09-04 at 11.38.18 AM

I think that the lunch room capture did better than the office capture near a window or the outside/ sidewalk capture because the light was flatter.  I’ve noticed that the program seems to have trouble with both shadows and also bright highlights.  Which is why we decided to try taking photos one more time at my place, with my Cannon 20D SLR camera, late in the day so that the light wouldn’t be more even.  The below images are some of what was shot, to give you an idea how we were going about this.  I went all around him, then got up on a step ladder and got shots all around from above.  I made certain to get the top of his head, since we’d had trouble with that in a previous attempt.  I got down low and shot upward to avoid any blank spots under the chin or hands.  I took closer shots of the hands and legs and feet to prevent a previous effect I’d seen where the legs and floor between them had been treated as a continuous object.

ernest**

I think that we had the right idea here, but I’ve since learned that the software relies a lot more on background overlap than I’d imagined.  So while I was sure to get overlap in my shots of Ernest, I didn’t think about making sure that trees were identifiable in the background from one shot to the next, or that I include the kind of overlap on the house that would help the software align shots.

My error became clearer when I tried to crop all of my images down to just Ernest, thinking that it would focus the software on the intended subject, but my results only became worse for doing so, and as I read more about it found advice to the contrary.  If I were to do this again, I would put clear identifying objects on the ground near my model to help the software key.  And I certainly wouldn’t have let the ladder ever be in different locations for different shots in the background.

I would like to try this again sometime with better attention paid to my lens as well.  While I wasn’t using a telephoto lens, I did have a moderate zoom lens on and I’m pretty sure I must have adjusted that between shots a little.  I also wonder about how the depth of field affected my results.  Sometimes there’s only so much you can do, especially shooting a tall lean figure like Ernest.  But I’m sure that as broad a depth of field as possible would be better.

Ideally, I’d have something like 60 cameras set up all around to cover all angles and on different colored tripods to help the software key each shot as it makes it’s shape, all firing at exactly the same time.  I could capture action shots with a set up like that, and skip the race against the setting sun entirely.  But I still think there’s possibility to get somewhere with what I do have.

Anyway, I had to move on to another method of doing things for my work project, but my interest in figuring out this technology remains.

Written by Sara

September 4th, 2013 at 10:42 pm

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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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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