Team:SUSTech Shenzhen/Hardware/Light

Light Modulator

Let there be light!

• 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 special direction . All devices are attempt to modulate the spatio-temporal pattern in a 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. Due to these proteins are sensitive to the wavelength of light, it is necessary to purify light of the projector.

Fig. 2 Spectra of protein in genetic circuit

Fig.1 Schematic of fluorescence microscope

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

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Optical Design

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) function as 1024*768 electronic shutter in each channel. Projector's super high pressure mercury lamp function as a high-intensity light source[Fig. 3].

Fig. 3 The projector structure. A)Parts of projector: Super high pressure mercury lamp, 3LCDs, Original Len. B) Light path inside 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 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. 4B) According to the principle of fluorescence microscope, corresponding Di-Mirror 89402bs and emission filter 89402m are install inside the microscope filter wheel(Fig. 4C). You can see all filters we use in our project(Fig. 4).

Fig. 4 A) Spectra of filter and mirrors are used in our system. B) Filter ET630/20X is for Chrimson, and Filter ET480/20x is for CoChR. Both these are installed outside 3LCDs. C) Di-mirror and emission filter are installed inside microscope

Fig.5 Play movie on hand.

To use 395nm light, red light and blue light at the same time, they are merged by a double LH Adapter, contained a semi-transparent mirror. Double LH Adapter connect to microscope. (Fig. 6) However, based on the optical principle of microscope, the light should image on the plane of Double LH adapter. To project whole image to microscope, it mean that image from projector should be about 5cm*5cm on plane. As all we known, normal projector will image in much longer distance and bigger than requirement. A new and cheap len Dukane 3inch/2.5 replaces original lens. The focus distance of [http://www.ebay.ph/itm/141444870051 Dukane 3 inch/2.5] is 3 inch(75mm). Every pixel in LCD is considered as single point light source, and using \frac{1}{f_{len}}=\frac{1}{D_{len-LCDs}}+\frac{1}{d_{len-adapter}} to estimate position of lens. Lens help us to smaller the projector's image to microscope(Fig. 5). Finally, we can control every pixel of image on specimen from projector.

Mechanical design

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 Apparatus to merge projector and microscope. Tube Lens Holder is used to hold new lens.

To build dark environment, we also build a dark room with cloth. Here will be 3D model and real picture.

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Control Software

Fig.7 Use Libreoffice for excitation.

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.

Fig. 8Community with Andor Company

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.

Fig. 9 The design's flowchart of ColorMapping . Image display in user interface from camera by Lima with Andor SDK3. User can track worm with some parameter. Then software generate image and project into microscope from projector. Finally, camera captures these pattern.

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Arduino Modulate Mercury Lamp

Fig. 10 Demo

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

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 PCB of Arduino modulate Mercury Lamp

Overview of Arduino modulate Mercury lamp(A) Arduino transfer the pulse command to servo. (B)The interview of Mercury Lamp.The servo fix at the original bottom. (C) The beam expander with filter connect to stereoscope

The result can be found in behavior result part.

Optical Fiber Light

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Bill

Here are detail bill.

Arduino Modulate Mercury Lamp

Parts	Unit	COST/unit ￥	COST ￥
EPSON	1	3960	3960
CNC Components	1	600	600
Precise 3D-print Component	1	213.22	213.22
Optical plate	1	230	230
Lifting columns(GCM-2211)	3	210	630
Arduino nano v3.0	1	13.50	13.50
Tower-Pro Servo	1	8	8
Filter 89402bs	1	3159.45	3159.45
Filter ET480/20X	1	2161.73	2161.73
Filter ET630/20X	1	2161.73	2161.73
Emission Filter 89402	1	2161.73	2161.73
		TOTAL COST	15299.36

References

Made by from the elegans.Inc in SUSTech_Shenzhen.

Licensed under CC BY 4.0.

• ©2017 SUSTech_Shenzhen