Posts tagged ‘economy’

There are  budget cuts and layoff everywhere. We have already heard before that Florida State dissolved academic departments to fight the financial crisis. And now the University of Florida is going to eliminate Computer Science Department, a really disturbing move. From Steven Salzberg’s blog:

The University of Florida announced this past week that it was dropping its computer science department, which will allow it to save about $1.7 million.  The school is eliminating all funding for teaching assistants in computer science, cutting the graduate and research programs entirely, and moving the tattered remnants into other departments.


We have recently begun to work on a project that requires us to find out whether a zebrafish larva can see or not. To this end, we have built a small machine to check whether the larvae show a visual behaviour called the optokinetic response (OKR).

This video shows the OKR machine, which is essentially a drum with black and white stripes that the rotating direction is controlled by a motor.


The fish larvae will be immobilized in thick solution in a Petri dish, which will be put inside the drum. The larvae with normal vision will be able to track the stripe rotation and move their eye balls. In this video, the bottom larva shows a normal OKR, while the top one does not show an OKR. It does not show an OKR because it is a blind mutant. An air bubble is put on the left to reflect the direction of the stripe movement.


During the process of fabricating this machine, we had come across with another cheaper way to do the same thing. There is a type of ancient Chinese lantern that part of outside drum will move due to heat convection generated by the light (A picture can be found in this Chinese article). We bought a contemporary version that the moving drums are driven by a motor. The type that we bought has the moving mechanism for rotating in opposite direction. We then took apart the lantern and used the moving mechanism to drive the opposite rotating stripes. See the following video for the moving mechanism of this alternative version of OKR.


Even though it is not perfect, it works! The most amazing part is the difference in the cost of fabrication.

  • The OKR machine made from Chinese Lantern: ~ $US 3 (for buying the Chinese Lantern)
  • The OKR machine that is made as shown in the first video: ~$US 150 (for materials) + ~$600 (for labor) = ~ $800 (and that does not include the controller box) !!!
  • A turnkey solution from a company costs > $40,000!

That is actually another example of the difference in the cost structure in doing research between the East and the West!

I also had a lot of fun sourcing other cheap parts for the final setup. For example, I have bought a very decent eye-piece camera for less than $40 (the price seems to have gone up a bit since then… but it is still very cheap) to capture the video of larval eye movement as shown in the second video. I have also bought a very economical ring light from AmScope for less than $60 for illuminating the drum area finally.

We are going to use this assay to identify fish with eye problems and then characterize the underlying molecular defects. That will help us study and find cures for the same diseases in human.


These days with tight budget and poor economy, I am always intrigued in finding ways to conserve my research funding, which I think is a responsible approach to research rather than the big spending and throwing-away-old-but-good-equipment mentality. For example, all monitors in my office are old, unwanted CRT monitors. The oldest one is a Sony Trinitron that I picked up as a postdoc at Harvard in 2004, when they were throwing away many CRTs and replacing them with the sexy LCD monitors. It is still running great and I wish I could pick up more at that time.

Anyway, there is an interesting new consumer camera called Lytro that has just been launched recently. It is based on a revolutionized light field concept that can capture not just the color and intensity, but also the vector direction of the light. Thus, information with regards to the location of the object be extracted after image acquisition; in other words, one can “focus” after image acquisition in the computer. This concept is originated from the Ph.D. research of Ren Ng, Lytro’s CEO, at Stanford.

I think the concept can potentially be applicable to research imaging in life-science. For example, in fluorescent imaging, we always want to acquire information from a very specific focal plane of the specimen. One fancy way to exclude the out-of-focus information is by confocal microscopy,  a fancier way of imaging which is not a cheap at all. From my limited understanding, Lytro’s principle can potentially be applicable to generate an effect that is similar to confocal on a regular fluorescent microscope, perhaps with some essential modifications of the algorithms. If that is possible, then Lytro can be a very economical replacement (a few hundreds) of confocal (hundreds of thousands). I immediately emailed them about that and asked for the possibility of getting a unit to play with. Of course they said thank you for the great idea, but no, we won’t be able to send you one.

I do hope someone, including Lytro, who has time and interest, can figure this application out… then we can have a $400 confocal! Think about capturing all the confocal market in the field!