dusjagr labs

Leaving cellsbutton / Heading for PlayAround10

dusjagr — Fri, 06 Aug 2010 00:39:46 +0000

cellsbutton#04 is over… or at least for me, and for this time. who knows when i gonna be back to wora wari. it was quite sad to leave earlier before the festival really ended, missed the day at the beach, missed the breakcore_labs.

but the next thing is already coming up, one night in singapore and a nice visit to Post-Museum, in little india, where we could a hardware/bio-hacking workshop next time, when passing through singapore. now finally heading to taipei and getting prepared for Playaround 2010 – DIWO culture

a day off from the cells…

dusjagr — Sun, 01 Aug 2010 18:44:16 +0000

After the busy last few days at cellsbutton#04, I took a day off and drove down to a beach near Tepus, Yogyakarta, maybe it was named Pantai Sepanjang… awesome biodiversity at the reef, millions of weirdest animals and colors, and all that completely alone with my friend u.

new GEM version of hacked mouse, thanks to Budi

dusjagr — Sat, 31 Jul 2010 19:11:39 +0000

After presenting the hacked optical mouse to a few people at HONF during the cellsbutton#04, Yogyakarta International Media Art Festival, I have been working with Budi aka vj manticore, from DeadMedia.fm on improving the pd patch to use GEM for the visualization. Muuuuuch better now, than my earlier canvas spaghetti code, thanks a lot Budi!

With the new implementation we can now use the whole spectrum of live image processing and analysis, like openCV for motion tracking, or additional sound synthesis. hope to jam the worms soon…

download the new files here:
worm_on_mouse2pdGEM_v1

dusjagr is back to cellsbutton

dusjagr — Fri, 30 Jul 2010 19:14:55 +0000

Niiiiice, I am back to cellsbutton#04, organized by HONF… the best festival ever!

The first few days were already busy, lots of interesting workshops, parties and discussions. also i met a lot of people, both new but also good old friends. I already got some first soldering action, and tried ways to make a diy version of the diy makeaway bitbadge. sadly i got the wrong site of pcb and cant use the shim for screen printing the solder paste. but with some patience we managed to get a few going…

also had some talks and workshops about new hackteria tools, such as the hacked optical mouse and the hacked PS3 eye mounted on an old microscope stage. i worked with akbar, a young microbiologist from UGM, on it and tested the DIY3 eye microscope for use with a haemocytometer to count yeast cells, which we then presented at the workshop at UGM later.

I was also happy to finally meet Georg Tremel again, from biopresence. He got some great recent work on DIY plant tissue culture and uses it with a blue flower, which is genetically modified for aesthetic reasons. He also did a workshop at UGM and hopefully the “Moondust” will grow there soon… and we got to have him collaborating for hackteria soon!

Talk about “Hackerspaces” @ plexwerk

dusjagr — Sat, 19 Jun 2010 17:38:37 +0000

Today I had a talk at the Plexwerk Tagung ‘transfer’ in Basel, where I presented some ideas about hackerspaces between digital- and biotechnology.

the slides can be downloaded dusjagr_plexwerk_hackerspaces_draft_2

I also wanted to show this movie about design of cellular patterns…

DIWO_chip Hackteria, Bio-Inspired Arduino Clone

dusjagr — Wed, 16 Jun 2010 17:15:52 +0000

Worm Filter 1.0

dusjagr — Fri, 04 Jun 2010 12:17:08 +0000

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…

New results on worm detection by hacked optical mouse

dusjagr — Fri, 28 May 2010 13:58:45 +0000

For more information about this project check the recent posts on this blog.

I just updated the pd-patch and the serial communication with the arduino. it now allows the frame-grabbing of the full 18×18 pixels from the mouse sensor, adns2610, with a reasonable framerate of 8fps. see download link below.

in addition i used the hacked optical mouse to detect the motion of nematodes, anguila aceti, and got some really clear results, both in the quality of the image and a substantial change in the SQL value. due to some grabbing issues when recording the screen the values are a bit delayed in the image above.

Download new code
worm on mouse 2 pd v1.1
worm_on_mouse2pd_v1.1

update for adns5020_datasheet, 15×15 pixel, 7 bit

Motility detection of microorganisms using a hacked optical mouse

dusjagr — Mon, 17 May 2010 08:18:22 +0000

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 18×18pixel 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 18×18 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):

worm_on_mouse2pd

* 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.

More hacks on the BioNano-Mouse

dusjagr — Thu, 13 May 2010 18:18:44 +0000

I continued on the hack of the optical mouse, first i installed an RGB-LED to be able to choose the color of the illumination. The using the blue LED i tried to detect fluorescence using a fluorescein solution. I got some signals, but still need to test the amount of reflected light and fluorescence. got some filters laying around somewhere… i could easily detect the loss of fluorescence, when following a tiny little drop that dried out, see image below.

Furthermore I improved the code to read out the registers for the frame-grabbing. it seems there is a limit to at what speed i can dump all the pixels of the frame. But still i could improve it by reducing some of the delays down to 1 µsec. It lookes much smoother now, but haven’t checked the worm yet.

Also i hacked another chip, the Avago 2610, very similar, 18×18 pixel array, And looking at the datasheet I should be able to get a lot more data out, such as, maximum and average pixel intensity, shutter speed, info about focused image etc.