Hey! This thing is still a Work in Progress. Files, instructions, and other stuff might change!

The 100 $ lab: Fluorescence microscope & behavioural tracker for optogenetics

by BadenLab, published

The 100 $ lab: Fluorescence microscope & behavioural tracker for optogenetics by BadenLab Jun 30, 2015
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5884Views 1072Downloads Found in Biology


Note: Any tips will go straight to our charity "TReND in Africa" (www.trendinafrica.org) which is dedicated to fostering university level science education on the African continent!

// note update v29 in scad (5th Aug 2016), has lower tolerance for all slidy bits to work well on an ultimaker 2. also the size of the PCB slot has expanded to reflect the latest iteration of that. The STL arrangements are still from version 26.

The 100$ lab: A 3-D printable open source platform for fluorescence microscopy, optogenetics and accurate temperature control during behaviour of zebrafish, Drosophila and C. elegans.

in collaboration with Andre Maia Chagas (ID: iamchagas) Lucia L Prieto Godino (ID: lprietog) and A Arrenberg

Hack-a-day link: https://hackaday.io/project/5059-flypi
Link on my page, including a work-in-progress manuscript + manual:

We call it "FlyPi", as it is based on a Raspberry Pi, and was originally intended for work with Drosophila (fruit flies). However, also without flies it is a very useful tool, e.g. for science teaching.

A Raspberry Pi 2 with adjustable focus RPi Camera module serves as the basic imaging unit. A custom Arduino Nano / PCB breakout allows flexible attachment and software control of a range of sensors and actuators. By default, it controls a bunch of LEDs for lighting, fluorescence excitation and optogenetic stimulation as well as a Peltier element and thermistor for accurate temperature control. In addition, servo motors and other actuators can be attached. All mechanics are 3D printed. A custom Python3 GUI controls both the RPiCamera and all peripherals through the Arduino.

As can be seen in the preliminary figures included, the system resolves things down to the size of single red blood cells and gives fairly descent GFP-based fluorescence images. Optogenetic stimulation of ChRII and ReaChR works, and we are currently optimising out Peltier control system (it overheats too quickly).

Notably, the videos don't do it justice - youtube kills the high resolution, both temporal and spatial, and introduces unfortunate compression artifacts. Original videos taken are crisp 5MP at 15 Hz, and go up to 90 Hz at x4 binning.

We aim to formally publish this in a scientific outlet in the near future, together with adequate documentation to build your own. The system can be assembled from off-the-shelf components that total ~100 $ (hence 100$ lab...). All plans & code are fully open. For now, however it's very much a work in progress and we are still working out the kinks... but do watch this space!

Also, do check out our recent publication on 3D printing lab equipment. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002086

Finally, do check out our Science & Africa NGO:


Here, amongst other things, we aim to implement these types of designs in science education and research on the African continent.

Andre's Site: http://openeuroscience.com/

Some videos:
Overview: http://youtu.be/T9DAaXVszYQ
Motorised focus: http://youtu.be/nKvuao8ENtA



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I am speechless! I am certainly going to give it a try. Please keep us informed with any tricks/challenges that you experience.

Thanks for posting!


Thanks. We are still working on this. Also we just opened a dedicated page for these projects which will probably be kept more regularly updated than the thingiverse version: www.Open-Labware.net

Dec 7, 2015 - Modified Dec 7, 2015
VidalGadeaLab - in reply to BadenLab

Wonderful! Thanks. I looked at the website and it is very impressive. Potentially a real game changer, as evidenced by the many downloads. We will give it a go. Eventually our goal will be to integrate this with a tracking system driven by another of your projects (http://www.thingiverse.com/thing:239105). Combined, the two system would pretty much allow us (and other labs) to perform the majority of behavioral experiments we carry on in our labs (and then some). Particularly impressive because I worked in a lab a couple years ago where this combined rig was purchased for $45,000. If this setup did a fraction of what our other setup was capable of it would really bring state of the art molecular techniques to many non-R01 labs. Keep up the fantastic work. We'll let you know when we have a working model :-)

Parametric 3 axis manipulator - optional servo mounts*

How did you track drosophila movements? Which software did you use for that?

Thank you very much tbaden. I'm going to try this software with protozoa