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Amira 3.1 and Movie Maker issues

Many thanks to Don Duncan at Mercury Computer Systems for his help getting the Movie Maker functionality back up and running on my system.

Problem: The Movie Maker module doesn’t work under Fedora FC4/Amira3.1.1. Part of the console error displays:
/path/to/amira/arch-Linux-Optimize/libmpegenc.so symbol errno, version GLIBC_2.0 not defined in file libc.so.6 with link time reference
Bad type "HxMovieMaker"

Solution: Don indicates other customers have had issues running Amira 3.1.1 on version of Linux later than Red Hat 8 (platform Amira was built on). The work-around is to set the following environment variable:
It has something to do with newer versions of the Native Posix Thread Library. The environment variable tells the system you want to use the older implementation.

If you’re running Fedora you probably don’t want to set the LD_ASSUME_KERNEL=2.4 as a default environment variable, so it might be better to manually set it if you know you’re going to need it in Amira.

Digital Fish Library in the news!

The DFL is in the news again!

Included in the most recent updates: News segment from NBC 7/39 in San Diego, and the press release at the SIO website.

Also, link to our little spot in Nature (one of the most prestigious scientific journals in the world). Nature 440, 396-397 (23 March 2006)


Digital Fish Library Press Release

Today is the big day – our press release is now out, and even featured on the SIO (Scripps Institution of Oceanography) website. In just under an hour we’ll begin scanning a juvenile great white shark as part of the press “event.”

If you haven’t read my other posts on the DFL, here’s a brief recap: We’ve been given an NSF grant to digitize most genera of marine fish (some freshwater) in the world using magnetic resonance imaging (MRI). The end goal of this has several application points: 1) Fish anatomy is digitized, so researchers can perform virtual dissections and explore the fish’s organs without physically destroying the real specimens; 2) These data, along with software tools we’re creating, will be used as teaching tools in high school education programs, provided by the Birch Aquarium as Scripps, 3) the availability of data will encourage conservation practices, as destroying real tissues will become less and less a necessity to perform common anatomical research – something especially important when dealing with rare specimens.

The press release is at http://scrippsnews.ucsd.edu/article_detail.cfm?article_num=718

More importantly, the DFL website is located at http://www.digitalfishlibrary.org/


Mac Trojan: Leap-A (OSX/Oomp-A)

There’s some news last night about the first Mac OS X “virus” in the wild. First of all, it’s NOT a virus. It’s a Trojan horse, which requires the user to execute the program him/herself. It’s low-risk and probably won’t spread beyond the few people who’ve already been infected. Good news is that it appears to be broken and doesn’t seem to do anything malicious.

Here’s a fairly detailed explanation of the trojan:

Here are a few tips you can use to protect yourself from this and other attacks in the future (adapted from an email I sent several of my Mac loving friends and colleagues):

  • Same as in the Windows world: If you don’t know what the file is, or where it came from, don’t open it.
  • Make sure your Mac OS X software is up to date.
  • Make sure you have a non-blank password on your user account.
  • In Safari, go do the preferences (Safari -> Preferences…) and click on the “General” tab (in Mac OS 10.4, should be similar in previous versions). UNCHECK the box that says “Open ‘safe’ files after downloading”. This is big, folks. Make sure you’re the one opening downloads, not Safari. It’s a little less convenient to have to open your downloads folder and open the file, but at least you have control over what gets opened and when.
  • From the open the Finder Preferences (Finder->Preferences…) and select the “Advanced” tab. Check the box, “Show all file extensions.” It’s not as pretty, but you’ll be able to immediately spot something like Leap-A: A JPEG image file should end with .jpg
  • Unless you know the program to be safe, don’t enter your password when an application requests it.
  • Keep regular backups just in case anything from this trojan or any other does something bad to your computer. I typically keep weekly backups to an external firewire hard disk drive.

Moral of the story – just be careful

Press Release

Keep an eye out in two weeks for a press release of the DFL. In two weeks we should have a pretty good beta up and running… sort of? It’ll depend on my other responsibilities at work.

The beta is up and running right now: DFL.

Things left to do for this revision:

  • Tie-together a couple back-end administrative tasks
  • Content, content, content
  • More/tighter integration with the DFL data view app that German is working on


Well, as my situation at work would have it, German (coworker), Larry, and I are working on a paper to submit to Siggraph for our work on the DFL. The deadline is Friday.

In the event our paper isn’t accepted, we’re going to look at doing a poster or talk.

Wish us luck!


First off, I don’t want people to think I’m some kind of web genius or something. I’ve been doing web design in my spare time (save my college years when I really didn’t have the time), since 1995, and it hasn’t been until recently that I’ve put much more effort into developing my skills. Designs are getting better and I’m very pleased with my self-taught PHP skills.

That said, I haven’t really had much chance to dabble with CSS until this past fall. I’ve used it many times for simple styling, but never serious layout. After struggling with some layouts ImageReady prepared from a mockup, I decided it was time to leave the table behind (except for the exact sliced image layout). I must say that given the same amount of time trying to get both methods to work, I was considerably farther along using CSS than I was with using tables. Even better, the code is so much cleaner – expected for a CSS project. I love CSS!

Is anyone reading this blog, by the way?

New DFL site coming

Feb 2 is the tentative due date for the DFL rewrite. Actually it’s the first phase of the upgrade, which will bring it up to speed with the current site in many ways. Additional functionality will be added every few weeks after that.

One of the biggest new features in this update will be the addition of the MRI dataset viewer/rendering application. Let’s just say this is groundbreaking work – the first time anything like this has been done successfully on the web. My coworker, German (yes, that’s his real name), has been working very hard on this application.

DFL update

My boss wants a nice looking front-end to the new DFL site, even if all the links are broken, so expect something next week. As it currently stands the new design is going to borrow heavily from the current one, though it should use space a little bit better and display information a bit more logically. You can see the current site at http://www.digitalfishlibrary.org/. The new site redesign is taking advantage of the Smarty Template Engine, so expect to see some Smarty tutorials in the near future.

Essential PHP Security

Just received Chris Shiflett’s Essential PHP Security book in the mail today. If it’s like the other O’Reilly books it should be pretty good. It’s pretty short – a smidgen over 100 pages, so it’ll be a good quick read.

Plan on seeing practical examples of how to apply these security techniques – here.

Merry Christmas!