Anatomy and Art

a blog by Sara Egner

Archive for the ‘technology’ tag

Record Breaking DNA Data Storage This Month

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Ok, wow.  Apparently we’ve got people who’ve figured out how to use DNA as basic data storage.  It sounds like they’re setting up a binary system, something like ones and zeroes dependent on when you have adenine and thymine pairs or when you have cytosine and guanine pairs.  And with just that, geneticists George Church and Sriram Kosuri at the Wyss Institute for Biologically Inspired Engineering in Boston, and Yuan Gao, a biomedical engineer at Johns Hopkins in Baltimore have apparently managed to record a whole book, complete with eleven illustrations onto a strand of synthesized DNA.

Nature Magazine has the story here.
Or you can go straight to the scientific publication if you have access here.

Written by Sara

August 25th, 2012 at 9:08 am

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Histological Visualization

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Perusing through some news today I found a few articles siting new software that is bringing 3D visualization into the histological realm.  Basically they are taking histological slides and using the same type of algorithms that CT and MRI use to generate 3D images that can be moved about in space and studied.

Reading these, I was really surprised to hear that such a thing hadn’t already existed.  It seems like something that you could do with Mimics honestly.  But I suppose it was the actual data collection at the microscopic level that wasn’t quite available.  Without a scanner doing the registration for you, one is left with having to work out each individual slide’s relationship to the next, and that could certainly eat up some time.  But Dr. Derek Magee at the University of Leeds seems to have found a good way of handling that.  So the person using his software scans in prepared slides, and the alignment happens automatically and a 3D image is presented.

I find it puzzling that these articles about the technology keep referring to the scanners as “virtual slide scanners.”  It doesn’t sound like there is anything “virtual” about them aside from the end result they produce of allowing a virtual 3D image.  Every description seems to talk about an actual physical slide being scanned for digital information.  That sounds like a scanner to me.  But I leave that one up to any of you reading to decipher whether you think I’m just missing something, or someone early on was quoted while trying to push technological buzzwords.  In my experience, either of those things could easily be true.

The work has been published in The American Journal of Pathology but is also discussed in these articles.

http://www.news-medical.net/news/20120417/Novel-system-for-3D-reconstruction-and-examination-of-tissues-at-microscopic-resolution.aspx

http://medgadget.com/2012/04/researchers-develop-3d-visualization-method-for-microscopic-histopathological-specimens.html

http://www.medicalnewstoday.com/articles/244203.php

*image above is from a traditionally prepared histological slide*

Written by Sara

May 6th, 2012 at 2:06 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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Thoughts About Web Design and Selling Art

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So after making a sale so quickly on that last painting, I’ve been giving a little thought to the power of these here internets, and how I can use that connectivity to make more sales.  As it is, I went back to my primary website where I’ve been keeping a record of everything I’ve put to canvas since coming back to painting in 2001 – http://snapshotgenius.com/paint.  It’s not really set up for sales, but I have always kept a record there of which pieces have been sold or given to someone.  That information presents in the single image view for any piece.  I went back and specifically put the words “available for purchase” on all the other ones though, to make that clearer.  Ideally though, I’d like to come up with a site where anyone interested could just buy a piece right then and there, or at least contact me directly with ease about pricing.  I wrote up a few scribbles about how I might go about this yesterday while I was thinking about it.

That’s the basic layout I came up with.  The one drawback I guess is that I never get to show off any of the pieces I’ve done as gifts that way.  I’ve got a few that I’m pretty proud of that fall under that category.  I’ll have to think about that some more.

This is usually about the point that I shake my head a bit and think about how narcissistic this whole process is.  And that pretty much goes for art on the whole, not just promotion.  Sometimes I feel like a little kid clamoring for everyone to look at me, look at my picture.  But it’s what we do.

Unfortunately, I’m not that great at web design.  All those little colons and semi colons all having to be just so, well it’s not exactly a strength for me.  Even if I was better with basic design, I know it’s another step entirely when you start bringing credit card transactions into the picture.  People do it though.  Maybe someday it will be a worth while investment for me to get someone to put that together for me.  In the meantime, I’ll keep scribbling notes about such ideas down for later reference.

Written by Sara

May 17th, 2011 at 7:18 pm

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A Long Saga of Gimbal Entrapment and the Horrors of Hotfix 4

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Oh Readers,

Last night I think I broke my brain again.

It took me  a week to get that rotational issue settled.  I went from trying various gizmo alignments, to scouring tutorial after tutorial, and then basically waving my arms in the air begging for advice from the world, which lead to a focus in learning how to set up helpers and then when that didn’t work, going through every rotational instruction I could find.  In the end, I used the Euler rotations from the pull down menu and changed the settings from the standard XYZ to ZXZ.  This spins your object off in a new direction, but I readjusted the object and was  finally able to control it’s rotation again and finish the shot.  To me, this seemed like a positively insane solution.  According to the readings I must have been gimbal locked, and resetting the orientation gave me a clean slate of sorts.  At least that’s my current understanding of it.  I could be way off base.

Regardless, this was a difficult saga for me.  So what a relief to finally be through that and rendering the shots already, right?  But then the renders kept crashing, and after the third error report sent to Autodesk I get this update recommendation.  So I click to install it, and the next thing I know, my project looks like this…

So much for going to bed then right?  Now I know that the worst thing that you can do in the event of something like this is to panic, but readers I must confess, I hit panic mode last night.  It had finally been working and then just like that, boom, blackness, and my entire grad school experience flashed before me, and I didn’t know what to do.

Apparently the update was the Hotfix 4 from Autodesk, and it’s done this to a few other people as well.  Advice ranges from uninstalling 3DsMax entirely and reinstalling without the upgrade to changing the graphics drivers away from the recommended system in the preferences, or even upgrading or downgrading your computer’s drivers over all.  And well, this is the kind of talk that tends to make me feel in over my head.  This is the kind of talk that sends me tirading about the ruins of an overly technological society.

If you are reading this because you are having the same problem now, I can first tell you that going into preferences and the viewports tab and hitting the button towards the bottom of the window that says something about installing or changing drivers (it’s no longer in front of me), you can in fact change to the Open GL driver, and if you are running on 32 bit, I hear that you may want to select the Software driver (the link to where I read that here.)  Anyway, that will let you see again, but I found that my objects kept going away when I was trying to select anything in the scene in that mode.  So, while it does make you feel better that all of your hard work has not been lost somehow, it still doesn’t restore the functionality you had before the “upgrade.”

Well this morning I was able to get someone from Autodesk on the phone.  Under the student license, they don’t let you speak first hand with technical support, but the woman on the phone was nice enough to ask around herself for me and relay what she could learn.  As it turns out, you can actually uninstall the upgrade.  Get rid of it, and you can use the recommended 3D graphics driver again and get back to work already.

To do this, you go through the Start menu, the Control Panel, Programs, Then I believe it is Programs and Upgrades, and you can select the horrible mistake you made last night and simply uninstall it.  I don’t know if this is something that Windows generally offers for most upgrades, or only for some.  But it’s a great feature, and I think it makes a lot more sense than all the other workarounds.  Just remove the problem.  Yeah.

Oh, and if you’re struggling with rotations like I was earlier this week and last week, this is a good write up about how some of that stuff works.

I don’t know if this is helpful for anyone else out there, or if I’m just making myself look bad in a public forum by putting my technical problems and frustrations out there for all to see.  I suppose it wouldn’t be the first time for either of those to be the case.

Written by Sara

April 28th, 2011 at 12:28 pm

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The Skin Gun

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I bookmarked this a while back, but it looks like I never got around to posting it.  National Geographic did this piece on “The Skin Gun,” a new innovation for the treatment of burn victims.  It literally sprays the patient with their own stem cells and promotes skin regrowth and rapid healing.

The video itself is a little on the flashy side as it gets going, but give it a minute, the technology they are talking about is really exciting. Burn injuries are just so damaging. The idea of being able to basically airbrush on new healthy cells is just incredible.

Way to go Science!

Written by Sara

March 13th, 2011 at 12:59 am

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Rapid Prototyping

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One of the things that has been particularly emphasized in my anaplastology training is the usefulness of rapid prototyping.  Wikipedia defines rapid prototyping as “the automatic construction of physical objects using additive manufacturing technology.”  My own understanding has always been that it includes both additive and subtractive manufacturing.  Either way, you get to essentially print out 3D objects from a file, and that’s pretty cool.

For clinical usage, this is particularly helpful alongside a laser scanner.  If you have both, you can scan in casts made from impressions taken from patients, alter them digitally, and then print out the altered models for use in your own physical creation.  The catch is that technology is expensive.  The party line has traditionally been that rapid prototyping in particular is expensive.  But the touch of awesome is that those prices seem to be coming down.

At the clinic we have a CNC milling machine.  It’s a big deal.  Maybe just a year ago the clinic was featured in the news and that very machine was photographed to represent our cutting edge technology.  And it is useful in what we do.

Just a few weeks ago I was visiting Texas, and an old friend mentioned a 3D printing company where you could send your own files for manufacturing, Shapeways.com.  They charge by the square centimeter.  And it’s affordable enough for my friends to be using it to make game pieces. That’s clearly not as practical as having your own machine, but it does show a movement in accessibility.

Then just last week someone was posting an article from Cornell University on the AMI list about how 3D printing may soon be a household capability.  I have to think that whether or not that is the case, clinically at least, this technology is about to be very accessible. I’m glad that we are learning to use it now.

Of course all that being said, I haven’t heard a word about laser scanners coming down in price yet.  But knock on wood, it’s bound to happen too.  And I, for one, know a thing or two about digital manipulation.  All of my animation software is directly applicable to just such work.

This is something that I can do.

Written by Sara

January 12th, 2011 at 12:45 am

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Autodesk Nighmare

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Well, it would appear that that last bit of enthusiasm for 3DsMax was undeserved.  I worked in it for about two hours and have not been able to access the program since.  I am at present, a week behind in work from working my ass off on trying to fix this.  Autodesk has so thoroughly disappointed me with their technical support for students that I can’t help thinking I should have just pirated it.  I don’t see that I’ve gotten anything more than extra hassle for the money I’ve paid.

The installation support line is 918-747-9333.
They will tell you right off that they don’t do technical support though and since their regular guy is out, you get Doug.

Doug is at 918-770-0164.
I haven’t been able to reach Doug so far today.  He may have simply given up on talking to me.  I don’t know.

The regular guy I can only reach by email and I don’t know his name.  He thinks I should try this on different computers, but I can’t because I don’t have a room full of computers capable of running this stuff, and even if I did, my licensing is only toward one machine.  That’s the student license deal.  You only get one.  That’s why I bought this new computer.  I wanted it to be that one.

That guy also recommends Autodesk Customer Service at 1-800-538-6401, and I have spoken to them.  I may get a replacement sent to me.  But they can’t help me establish if that is the problem or not.

He also sent me to Autodesk Registration at 1-800-551-1490.  There a man named Rain sent me to the Douglas Stewart Co.  This was supposed to resolve any activation problems.

See I thought I might be having an activation problem now, because today I uninstalled everything from the Windows side of my computer including Windows and Parallels in the hope of starting over completely.  I was told that the problem may be my version of Windows.  I can’t exchange my version of Windows now, but I could buy a new one outright and see if that works.

By the way, the Parallels support number is 888-811-2489.

So after uninstalling *everything* on the Windows side I attempted to install on the Mac side of the computer the two programs that were working on the Windows side, Mudbox and Maya.  Mudbox loaded up just fine, but Maya keeps failing on exit, whatever that means.  So I suspected that the serial number was the problem and that it was showing the previous registration on the Windows side of my computer which according to Parallels shouldn’t have worked in the first place because of my Windows version and which now does not exist.

So getting back to the Douglass Stewart Co., they actually don’t handle anything of the sort.  The woman there could only give me the installation support line 918-747-93333, which is the number I started with in the first place.

I’ve probably spent the most amount of time with the people working for Parallels from India.  Their phone system is a little shaky, but two of the people I’ve spoken to over there have been very helpful.  Just no one seems to be able to fix the problem.  They are the ones now recommending that I purchase Windows 7 64-bit Professional instead of the Windows 7 64-bit Home edition I currently have.  I did research that before purchasing in the first place, but nothing online indicated that one would be better than the other so long as I was in 64-bit.  But the disks, now that I have them, do suggest Windows 7 Professional 64-bit (now that I have opened them), so maybe that is the problem there.

But regardless, Maya now won’t install on the Mac side of my computer, which has nothing at all to do with Windows, and points back at the Autodesk software possibly being corrupt.  Or perhaps my previous attempts to install have now done something to make  this not work.  I currently have Mudbox up and running, and that’s all I seem to be able to get.  I am currently waiting on a phone call back from someone named Barbara who may or may not tell me anything useful.

I’m quite certain I sound like a complete lunatic to anyone answering the phone at this point, and they would probably be right to think that.  Presently I need a shower, and I need to eat something, but I can’t seem to get around to either while I have all this in front of me.  It’s almost been a full week since I installed all of this, and it still isn’t working, and I still don’t know why, and I still can’t get the help I need.

This has become such a nightmare.

Written by Sara

September 16th, 2010 at 1:25 pm

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Technology

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Lately there has been a technological glitch between Firefox’s new Flash upgrade, and the design behind WordPress blogs which has kept me from being able to upload images here. For as much as we use technology to create the things we want, it sure does get in the way a lot too. Well I believe I just found the work around. So here is a nice big photo to celebrate…

That is actually one of my photos, as well as my hand (well the living one anyways). The bones were courtesy of UIC’s collection that gets handed out for reference among students taking Gross Anatomy.

And if any of you reading here are also bloggers and encountering difficulty uploading images to your own sites, I found the fix here…

http://wordpress.org/support/topic/217126

What they don’t tell you is that disabling the Shockwave Flash plugin will affect your browser experience in other ways.  In my case, I noticed that video goes offline when I have it disabled.  But what you can do, is disable Shockwave Flash for just the time it takes you to upload your images, and then go back and re-enable it.  Now that your files have been loaded, you can access them as you normally would.

There is little more frustrating than being blocked in our creative endeavors by technical errors and glitches.  Unfortunately, the more programs we bring into our efforts, the more common this problem becomes.  Just the trouble of our times I guess.

Written by Sara

August 4th, 2009 at 4:40 pm

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