AES Column “The Trailing Zone” by Victor M. Ugaz

A column highlighting broader perspectives and observations about science and the lives of those who pursue it.

Image Analysis

I had a completely different topic in my mind for this column until last Tuesday when something unexpectedly changed. The date was September 11, a time when most briefly pause to remember where they were, what they were doing, and how they felt on that morning in 2001. But this year something deeper was stirred that made me think back to that time eleven years ago in a way that I hadn‘t before. Since my story has an electrophoresis connection, the time seemed right to share it.

In 2001 I was in the midst of a postdoctoral appointment at the University of Michigan where my research involved studying microchip-based gel electrophoresis of DNA. My experiments required me to continually build and assemble new devices for testing, and I had established a good daily routine to accomplish this: finish device assembly in the early morning, run experiments and analyze data in the late morning/early afternoon, and begin initial assembly of the next day‘s devices in the late afternoon.

So it was that I spent the morning of September 11 in our cleanroom facility, using a wire bonder to make electrical connections in the chips I planned to test later that day. This instrument happened to be located near a window across from my boss Mark Burns‘ office. Around 9:30 am, I remember his tapping on the window and trying to tell me something. I didn‘t understand him (I‘m horrible at reading lips) so we both gave up and I went back to work. I now know that he was trying to say something like, “Did you hear what happened?”

If you haven‘t spent time in a cleanroom before, it can be a surreal experience. You are gowned up from head to toe in an environment where your senses can easily become dulled by the long wavelength lighting and continuous background hum of air handling machinery. It can really feel like you are in another place, somewhere far removed from everyday reality. This feeling was never more evident than when I stepped out of the gowning area later that morning and learned exactly what was going on. The world I had left behind when I entered the cleanroom seemed to have vanished.

A television had been set up in the departmental conference room where some gathered to watch the story unfold. I stopped by but didn‘t stay long. I made a decision that this was not how I wanted to spend the day. Instead, I was determined to carry on. To not let these events disrupt my life. But simply continuing with my routine of planned experiments didn‘t seem like enough. I needed something more. A more lasting record of my defiant stand. So that afternoon I proceeded to finish up an ongoing project aimed at streamlining the computer codes we used to analyze video recordings in our experiments. I then composed a lengthy email (shown below) to the group detailing these changes. There‘s nothing particularly remarkable about the message. The most interesting thing is probably the fact that 80 GB of hard disk space was at that time so huge that it was taxing our departmental backup servers. But to me it had a much deeper meaning. The email was not about image analysis at all. I clearly could have done that any time. It was instead fulfilling a more important need for me, to document that on that day, at that time, in the face of those events, I chose to carry on in my own way.

Although I vividly remember writing this email, I‘ve never gone back to look at it since that day. But this year, for some unexplained reason, I felt compelled to dig it up. Would I react the same way today? Probably not. I think I would instead allow myself to take in the emotions of the moment and not be afraid to meet them head on. Some doors close but others open, endings lead to new beginnings. I know this now but was not so sure about it then.

From: "Victor M. Ugaz"
Subject: Image Analysis Upgrade
Date: September 11, 2001 3:41:39 PM EDT
To: Burns Group

This e-mail is for group members doing video image analysis as part of their research.

Since more of us need to do image analysis on a routine basis, we are in the process of upgrading our capabilities in this area. Last week, Dylan upgraded the "Video Drive" on Vulcan to an 80 GB capacity hard drive. This will significantly relieve our drive space problems for now, but we need to continue to be careful about how many files we store. Some general tips are...

1. Capturing videos at half size (320x240) rather than full size (640x480) will significantly reduce the video and tiff file sizes and should be sufficient for most of our needs.

2. It is only necessary to keep either the raw video file or tiff sequence. Keeping both is redundant. If you keep notes about your capture settings, you can always go back to the original video tape later and reconstruct your analysis if necessary.

3. It's a good idea to continually go back and look at your files to see whether you really need to keep video files. A run that was good a few months ago may not be so good now.

The sheer number and size of files on the video drive has placed an excessive burden on the Department's routine back-up capabilities. Consequently, Dylan has removed the Video Drive from the backup schedule, and is ordering DVD-RAM disks for us to use to make our own backups.

Once those arrive, each user will be responsible for backing up his or her own files...

[The email continues with detailed instructions for the use of specific macro codes we developed for our analysis]

Lastly, Dylan and I are in the process of getting a duplicate video capture setup in place for the other PowerMac G4. This will be a big help in alleviating the bottlenecks we are now facing with video image analysis. I'll let you know as soon as we get that set up.

That's it for now. Happy image analysis!

Victor

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Victor M. Ugaz, Ph.D.
Postdoctoral Research Fellow
Department of Chemical Engineering
University of Michigan
3074 E. H.H. Dow Building
2300 Hayward
Ann Arbor, MI 48109-2136

Victor M. Ugaz is Associate Professor and K. R. Hall Development Professor in the Artie McFerrin Department of Chemical Engineering at Texas A&M University. Comments and suggestions are welcome.

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