Archive for the 'research' Category

Worm Filter 1.0

First experiments are underway of using simple geometrical micro-chambers in PDMS to be able to sort and seperate motile whole organisms. At the moment the students of life science technologies, FHNW, are investigating the device shown above, which exhibits 3 different triangular filters with varying gate dimensions, using Anguilla Aceti (Nematode).

a movie will be uploaded soon...

Motility detection of microorganisms using a hacked optical mouse

Just done further experiments with the hacked optical mouse sensor, in this case a Avago ADNS2610, from a cheap wired logitec optical mouse. So i managed to connect the optical sensor to the arduino and send all the data, including the image from the 18x18pixel sensor, through a serial connection to puredata (pd). The sensor is a real high-end device, it calculates the optical flow, thus gets out motion and the speed of the mouse, it detects focus by a SQL-value, which is proportional to the number of features the sensor detects on a surface. and other values such as maximum and average pixel and shutter speed can be read from the registers.

The frame rate of the transmitted image is sadly relatively low, cos the ADNS chip is not meant to present this info at higher speed. still its reasonable, when reading all 18x18 pixel a framerate of roughly 5 fps is feasible, if you only dump the first couple of lines you can increase it to higher framerates.

After building a patch to visualize all these data from pd, i started experimenting with placing microorganisms on top of the sensor, keeping the optics intact, but replacing the LED with an RBG, so i can control illumination.

I got some really amazing results, it seems i can detect single cell microorganisms using just the mouse sensor and an arduino. see the movie below. while the sensor only detects motion if the whole image is shifted, it seems that when a microorganism (Blepharisma Japonicum) passes the field of view, there is a substantial change in the SQL-value.

further i will try to do some simple image processing on the arduino directly, such as simple background substraction.

Download Code
The code for the arduino and puredata can be found here (work in progress):


* The arduino code, uses two libraries: pitches.h and SimpleMessageSystem.h. the first is just used to play a nice little welcome melody, the second is only needed to communicate back from pd to change the dumpWidth of the frame. copy them to your libraries folder.

* The pd patch uses two externals, "convert" to communicate with SimpleMessageSystem" (again only from pd to arduino not vice-versa) and a second one, "pd_fire_grad" to apply a look-up-table (LUT) to the pixels for better visualization.

Laser cutting session with urs aka hugi

I finally got around to see my friend urs aka hugi to test his living-room laser cutter. nnnnnice.. the democratization of manufacturing has started, home-fabbing rocks!

so we tried to cut tape glued on top of microscopy slides, to be used as master for casting PDMS microchannels, see my article on homemade microfluidics, to be published in chips&tips. with these structures i will be able to do nice practical lab experiments on microfluidics with the students from FHNW.

more than that, of course we had the laser power all the way up, cos its fun, creates a lot of smoke and is spectacular to watch. and it seems the laser cut right into the glass slides.... hmmm that looked like fun. so we spent the rest of the evening carving our custom made microsocpy slides, see pictures below.

of course we didnt stop there and tested the laser micro-projector, see older post, and could beautifully project through the glass slides and get a nice, sharp and clear image of the dusjagr icon projected on our neighbors wall. hmmm that also looks quite interesting.


experiments with the microscopic eye

After a discussion with some sci-fi movie makers in melbourne I thought i could show up at the set using my newest development...

The animals arrived

Finally the cultures arrived from sciento, UK. I got some amoebae, rotifers, tardigrades and a weird little japanese swimming thing i forgot the name of. they all seem happy and lively and obviously survived the travel in the mail.

first experiments using the webcam as a microscope revealed nice images, see above. and a newly made pd-patch allows me to record nice time-lapse movies to check out the amoebae....

first step in micro DNA injection

“To invent, you need a good imagination and a pile of junk.”

Thomas A. Edison
US inventor (1847 - 1931)