• Weight: 10kg
• Power:　200W
• Cost: ￥15299.36

Multiple devices of optics are designed and created for the various experiment requirements, such as stimulate neuron of C. elegans, train C. elegans and induce C. elegans move in a special direction . All devices attempt to modulate the spatio-temporal pattern in an elegant and effective way.

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Projector Light Source

Biology background in our project: We need 395nm light activate Calcium indicator protein GEM-GECO for neuron image. For the independent excitation of neurons (AWA and AWB) in C. elegans, channelrhodopsins CoChR and Chrimson are activated by blue light and red light^[1]. Due to these proteins' sensitivity to the wavelength of light, it is necessary to purify light of the projector.

Fluorescence microscope plays an important role in our experiment. The Zeiss Company creates a perfect visual animation to show how the fluorescence microscope works, and you can find it on their [http://zeiss-campus.magnet.fsu.edu/tutorials/basics/axioobserver/indexflash.html web]. However, typical fluorescence microscopes can only illuminate the specimen ( C. elegans) with the same light in whole view. There, we modify a consumed projector to a new light source, which can illuminate specimens locally, in multi-color, in multi-points and dynamically. The Projector Light Source also has short response time and high light intensity, which will be an effective, hackable and potential tool for synthesis biology.

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The design of optics

GEM-GECO is activated by 395nm light from LumencorSpectra LED Illuminator.

We use projector [http://www.epson.com.cn/products/projectors/239/CB-X03/ EPSON CB-X03] as red light& blue light source for CoChR & Chrimson. Projector's 3LCDs(red, green and blue channel) functions as 1024*768 electronic shutters in each channel. Projector's super high pressure mercury lamp functions as a high-intensity light source[Fig. 2].

Firstly, we need to purify the light of projector. Although original filter can separate white light into red light and blue light, the bandwidth of red light or blue light is not narrow as a requirement of our optical sensory protein(CoChR & Chrimson). We install additional red filter Chroma ET630/20X and blue filter Chroma ET480/20X outside 3LCDs. (Fig. 3B) According to the principle of fluorescence microscope, corresponding Di-Mirror 89402bs and emission filter 89402m are installed inside the microscope filter wheel(Fig. 3C). You can view all filters we use in our project(Fig. 3).

Secondly, the image of projector should be shrinking. To use 395nm light, red light and blue light at the same time, they are combined by a device, called double LH Adapter, contained a semi-transparent mirror. the double LH Adapter is connected to microscope. (Fig. 5) However, based on the optical principle of microscope, the light should image on the plane of Double LH adapter. To project the whole image to microscope, it means that image from projector should be about 5cm*5cm on plane. A new and cheap lens Dukane 3inches/2.5 replaces original lens. The focus distance of [http://www.ebay.ph/itm/141444870051 Dukane 3 inch/2.5] is 3 inches(75mm). Every pixel in the LCD is considered as a single point light source, and using \frac{1}{f_{len}}=\frac{1}{D_{len-LCDs}}+\frac{1}{d_{len-adapter}} to estimate position of the lens. Lens helps us to shrink the projector's image to microscope(Fig. 5). Finally, we can control every pixel of image on specimen from projector.

The design of mechanics

We need to install new lens on projector with adjustable component, and fix all device with microscope stably.

Lens Holder and Connection Tube are design(Solidworks Documents) by CNC and 3D-Print(Fig. 6).

To build dark environment, we also build a dark room with cloth(Fig. 7).

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The design of Software

Software is most flexible part. A very easy method is using slide(Demo Slide), such as LibreOffice(Test on 5.4.2.2.0+ in Arch Linux) or Microsoft Office. The image and time pattern is configured in slide, including color, intensity and pulse time etc.

We also develop a more powerful and hackable open source software suit called ColorMapping to track and activate multi C. eleganss or cell independently in one view. User can modify multi color, intensity, time and locations of light alternately in GUI. Everyone is welcome to join us to develop ColorMapping in GitHub, which still is developing.

ColorMapping, contains camera part, projector part, user&calculation part. It is coded by Python2, Pygraph, PyQt5, [http://lima.blissgarden.org/camera/andor3/doc/index.html?highlight=andor3 Lima(Library for Image Acquisition)]. ColorMapping tests on Arch Linux.

To drive Andor Zyla (5.2), we apply Andor SDK3 from Andor Company firstly. All data are matrix during data transfer and calculation. Camera image live in user interface. In camera part, exposure time and other parameters can be adjusted.

A important algorithm is how to project special area in special color. The key is coordinate system transformation between camera view(2560*2160) and projector(1024*768). To simplify question, only the left projector edge and 4 ROIs(region of interesting) are drew. Every point(X_{projector}, y_projector) in image will be generated from following formula. \left[\begin{matrix}x_{projector}\\y_{projector}\end{matrix}\right]= [\begin{matrix}{1}&{\frac{1024}{L}}\end{matrix}](\left[\begin{matrix}x_1\\y_1\end{matrix}\right]-\left[\begin{matrix}x_0\\y_0\end{matrix}\right])

In ROIs Setting, every ROI can set the color(Blue or Red) and intensity(0~255). The 4 ROIs can move by mouse in real time, so the projector can response immediately. Generated image is showed a full-screen window in another extended desktop. Projector is only the show extended desktop.

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Arduino Modulate Mercury Lamp

Biology background: To reduce the phototoxicity during train C. elegans, pulse of light is required rather than constant light^[2].

A simple and effective device to output pulse of certain wavelength of light. On time and off time of pulse is custom by Arduino. Wavelength of light is changed by replacing filter before beam expander.

The result can be found in behavior result part.

Optical Fiber Light

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Bill

Here are detail bill.

References

1. ↑ Lisa C. Schild and Dominique A. Glauser , Dual Color Neural Activation and Behavior Control with Chrimson and CoChR in Caenorhabditis elegans, 2015, GENETICS.
2. ↑ Venkatachalam, V., & Cohen, A. E. (2014). Imaging GFP-Based Reporters in Neurons with Multiwavelength Optogenetic Control. Biophysical Journal, 107(7), 1554–1563. http://doi.org/10.1016/j.bpj.2014.08.020