The Story of Our Hardware

Beginnings

As a first step, we defined our requirements:

• The illumination must be provided by blue LED (~450 nm wavelength).

• The brightness of the illuminating LED shall be controllable (dimmer function).

• Be suitable for various instruments (test tubes, Erlenmeyer flasks, and 96-well plates).

• It must be coolable. — Our previous experience showed that liquid significantly cools the cell medium too, so we considered air cooling.

• Be usable in multiple experimental configurations (e.g., side or bottom illumination mode).

• The illumination should be programmable in time, up to several hours, and in the intensity of brightness.

• Preferably, no unique expertise, such as knowledge of microcontrollers, is required to create the lighting program.

• The device should preferably not require special skills and tools to set up and repair (e.g., replacement of surface-mounted chips).

• Be buildable and repairable within a reasonable budget.

• And the most important: it must be safe. It should have no problems with touch protection, plus be waterproof if possible.

Then, we dug deeper into the literature on optogenetic instruments and commercially available devices.[1, 2] Unfortunately, we found that they did not meet our requirements. Which features are not beneficial for us:

• Usable for only one device (e.g., 96-well plate).

• Good for one type of experimental set-up (e.g., how can they solve a side illumination of a flask?).

• You need special microcontroller programming knowledge to write a lighting program (Raspberry Pi or Arduino). So you can't reprogram it to another brightness/lighting program in a few minutes.

• Creating a device is complicated and expensive (printed circuit board, surface mount component, custom fabrication). And it is beyond repair if there is an issue with it!

Based on the above, our team asked Tamás Englert, an electrical engineer who currently works in the field of IT, for advice on designing an optogenetic device that meets all the expectations.

LED strip

It initially refers to LED chips glued to a flexible, ribbon-shaped printed circuit board. It is cuttable at specified locations, usually 3 per LED. The backing is self-adhesive. There are single-color, multicolor (these have a variety of individual colored LEDs), white cool and warm light, outdoor, indoor, etc. In this guide, for simplicity, we will call all LEDs that are controllable together a LED strip. Even if they are one LED, even if they are soldered to a solid printed circuit board, or even if they are individually attached somewhere.

LED dimmer control

The brightness control is called a dimmer. It can be a wall-mounted dimmer, a simple remote control device, or a digitally programmable LED driver. Since the LED reacts instantly for turning on/off, it is typically ” switched” to change the brightness. Extended off states mean weaker light. The control is called pulse width modulation (PWM). The dimmer is controllable, usually by a small manual remote control. Interesting fact: there are many mobile apps for controlling infrared dimmers (searchable under LED remote). There are also infrared and radio-controlled. It controls one ribbon, so it has a maximum of 4 channels (due to RGBW LED ribbons).

Power supply for LED strips

They can be 5, 12, and 24 V, have individual housings, can be built-in, or have adapters (like laptop power). We're interested in the 12 V adapter format because it doesn't have contact protection issues.

Control channels for LED strips

A LED strip driver (e.g., dimmer) can control several LED stripes according to the configuration. One channel is required to manage a set of LEDs simultaneously. For example, some devices require this many channels: single LED=1 channel, single color LED strip=1 channel, tricolor LED strip (RGB)=3 channels, 96-well plate each tube individually with one color=96 channels, but if the same program per column is good, 12 channels (since there are 12 columns).

Instrument I: an Erlenmeyer flask/individual test tube illumination

To test our bacterial construction as soon as possible, we first thought about a device that would be quick to assemble and easy to use. Since programming interfaces, dimmers, power supplies, and LED drivers are easily obtainable, only one specific part needs to be invented for the experiment: the illumination area is required, where only the structure supports the LEDs.

Building elements

• Dimmer remote control (It can also be a mobile app!)

• LED strip dimmer (brightness control)

• 12 V power supply for LED strip and cooling fan

• 12 V PC cooling fan

• Blue LED strip glued to the inside of a cylinder

• The unique illuminating area is a cylinder to which the fan connects from the bottom, and the LED strip is attached to the wall.

Advantages

• Very cheap
  

  1 m blue LED strip, power, dimmer and remote control are under 10 000 HUF (=under $25.5). (The rate of exchange was calculated according to the currency of 2022 September.)

• Very simple and quick to assemble
  It can be assembled in about 1 hour without any expertise.

• Modular
  

  All elements are interchangeable, and lighting is available in a shop or webshop. Replacement of the modules does not require any expertise.

Disadvantages

• Not programmable
  

  You cannot create an illumination program. The experiment proceeds by switching on the instrument, adjusting the brightness with a meter, inserting the sample, waiting for the scheduled time, and switching off or switching off/on for a specific time. In other words, all steps are controllable manually!

• Low number of channels
  

  Sometimes it's not a problem, e.g., an Erlenmeyer flask requires one channel. But a 96-well plate illuminator controlled 96 per diode and 12 per column. And an apartment lighting dimmer has a maximum of 4 channels because of the 4-color LED strips.

Instrument II: RaccOpto, which can illuminate a 96-well plate

After hard work and learning, we have succeeded in creating an optogenetic tool, RaccOpto, that meets all our predefined requirements and has become one of the most significant parts of our project. We have continued to use commercially available elements, except for the custom lighting area. However, its elements are only briefly discussed on this page, as we are considering entering the market with it due to its great success among research groups.
We have created two easy-to-program lighting devices: one per column and one per row.

Building elements

• A PC

• A controller for the dimmers

• 12 V power supply connected to dimmers

• Special dimmers that give us the right number of channels

• 12 V PC cooling fan

• 96 blue LEDs

• The unique illumination area consists of 96 holes drilled in a 6 mm aluminum sheet, each containing a blue LED. The aluminum is responsible for heat dissipation, and a PC fan provides the cooling.

Advantages

• Still cheap (due to the factory modules)
  

  Building one lighting equipment costs the team approximately 120 000 HUF (=$295). (The rate of exchange was calculated according to the currency of 2022 September.)

• Very simple and quick to assemble
  

  Everything is modular, all elements are interchangeable, and lighting is purchasable in a shop or webshop. Replacing the modules does not require any expertise.

• Easy to expand
  

  Need more control channels? Buy four for 20 000 HUF (=$49.2)! Wire them into the network, set them up with the control software, and you can use them! (The rate of exchange was calculated according to the currency of 2022 September.)

• Easy to program
  

  The lighting program is quick to create and requires no expertise. Its graphical interface makes it particularly user-friendly. The factory software is free and available for several operating systems.

We hope that the story of our hardware will be inspiring for future iGEM teams, as it has proven to us that by working together and combining different fields of science, we can create something unique.

We would like to thank Tamás Englert for his creative ideas and expertise throughout Hardware's journey.

[1] Repina, N. A.; McClave, T.; Johnson, H. J.; Bao, X.; Kane, R. S.; Schaffer, D. V. Engineered Illumination Devices for Optogenetic Control of Cellular Signaling Dynamics. Cell Rep. 2020, 31, 107737. https://doi.org/10.1016/j.celrep.2020.107737.

[2] Bugaj, L. J.; Lim, W. A. High-Throughput Multicolor Optogenetics in Microwell Plates. Nat Protoc 2019, 14, 2205–2228. https://doi.org/10.1038/s41596-019-0178-y.