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{{ SUSTech_Image | filename=T--SUSTech_Shenzhen--lampmovent.gif| caption= Fig. 10 Demo}} | {{ SUSTech_Image | filename=T--SUSTech_Shenzhen--lampmovent.gif| caption= Fig. 10 Demo}} | ||
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'''Biology background:''' To reduce the phototoxicity during train ''C. elegans'', pulse of light is required rather than constant light<ref>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</ref>. | '''Biology background:''' To reduce the phototoxicity during train ''C. elegans'', pulse of light is required rather than constant light<ref>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</ref>. | ||
− | A simple and effective device | + | A simple and effective device output pulse of certain wavelength of light. On time and off time of pulse is custom by Arduino (A popular single-board microcontrollers). Wavelength of light is changed by replacing filter before beam expander. |
− | {{SUSTech_Image_Center_8 | filename=T--SUSTech_Shenzhen--PCB.png|caption='''The PCB of Arduino modulate Mercury Lamp'''}} | + | {{SUSTech_Image_Center_8 | filename=T--SUSTech_Shenzhen--PCB.png|caption='''Fig. 11 The PCB of Arduino modulate Mercury Lamp.''' Arduino's power is usb, and connect to a Servo Motor.}} |
{{SUSTech_Image_Center_fill-width | width=1000px|filename=T--SUSTech_Shenzhen--DSCF2143.jpg | caption='''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}} | {{SUSTech_Image_Center_fill-width | width=1000px|filename=T--SUSTech_Shenzhen--DSCF2143.jpg | caption='''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}} |
Revision as of 08:50, 1 November 2017
Light Modulator
Let there be light!
Contents
- 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.
Modulate 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.
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).
The design of mechanics
We need to install a 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).
The design of software
To control the ouput of light source, a software is required. However, a very easy method is using a 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 suite called ColorMapping to track and activate multi C. elegans 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 Python 2 Language, and third-party packages, PyGraph, PyQt5 and [http://lima.blissgarden.org/camera/andor3/doc/index.html?highlight=andor3 Lima(Library for Image Acquisition)]. ColorMapping tests on Arch Linux.
{{SUSTech_Image | filename=T--SUSTech_Shenzhen--LightModulator_andor.png | width=209px| caption=Fig. 9 Community 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 lives in user interface. In camera part, exposure time and other parameters can be adjusted.
An important algorithm is how to project a special area in special color. The key is coordinate system transformation between camera view(2560*2160) and projector(1024*768). To simplify the question, only the left projector edge and 4 ROIs(region of interesting) are drew. Every point(X_{projector}, y_projector) in the image will be generated from following formula(Fig. 10).
\left[\begin{matrix}x_{projector}\\y_{projector}\end{matrix}\right]= {\frac{1024}{L}}(\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 define the color(Blue or Red) and intensity(0~255). 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 just show on extended desktop.
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 output pulse of certain wavelength of light. On time and off time of pulse is custom by Arduino (A popular single-board microcontrollers). Wavelength of light is changed by replacing filter before beam expander.
The result can be found in behavior result part.
Optical Fiber Light
Bill
Here are detail bill.
Parts | Unit | COST/unit ¥ | COST ¥ |
---|---|---|---|
EPSON | 1 | 3960 | 3960 |
CNC Components | 1 | 600 | 600 |
Precise 3D-print Component | 1 | Arduino Modulate Mercury Lamp213.22 | 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
- ↑ Lisa C. Schild and Dominique A. Glauser , Dual Color Neural Activation and Behavior Control with Chrimson and CoChR in Caenorhabditis elegans, 2015, GENETICS.
- ↑ 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