Difference between revisions of "Team:SUSTech Shenzhen/Hardware"

 
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== '''1.''' Microfluidics ==
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              <h1 style="font-size:54px">Microfluidics</h1>
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              <p style="font-size:24px">A function to research <i>C. elegans</i>'s neuron activity and behavioral response  </p>
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              <h1 style="font-size:54px">Pump and microscope </h1>
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              <p style="font-size:24px">A platform to use microfluidics</p>
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              <h1 style="font-size:54px">Projector</h1>
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              <p style="font-size:24px">A custom light source to emit the blue light and red light </p>
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              <h1 style="font-size:54px">Microscope and projector</h1>
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              <p style="font-size:24px"> Play with light in spatio-temporal</p>
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In our experiment, we want to research neuron activity and behavioral response to Caenorhabditis elegans under the certain wavelength of light. Thus, we need to choose a clear, efficient and convenient platform to study not only a group of worms but also an individual one. Microfluidics has a very tiny scale, which is best matched with th size of C. elegans. We design three parts of microfluidic chips to achieve our experimental goals. We design a selective chip to choose appropriate sizes of worms, and use Gaussian chip to prove its olfactory receptor neuron pairs are normal. Finally, we immobilize worms to research the individual behavior and neuron activity.
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Detail in [https://2017.igem.org/Team:SUSTech_Shenzhen/Hardware/Microfluidics here]
 
  
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== '''2.''' Play with light in spatio-temporal ==
 
  
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Multiple devices of optics are designed and created for the various requirement of experiments. All devices are attempt to modulate the spatio-temporal pattern in a '''elegant''' and '''effective''' way. Just let us start to play with light.
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{{ SUSTech_Image | filename=T--SUSTech_Shenzhen--lampmovent.gif| caption= AMML Demo}}
 
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=== '''2.1''' Device One: Arduino Modulate Mercury Lamp--AMML ===
 
  
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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.
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{{SUSTech_Image_Center_8 | 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 connect to stereoscope}}
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= Microfluidics =
  
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In our experiment, we want to study the neural network activity and behavioral response of <i>Caenorhabditis elegans </i>under light stimuli of specific wavelengths. Thus, we need to design an accurate and user-friendly platform for studying the collective behavior of worms with high throughput as well as live neuron-level observations under natural conditions.
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=== '''2.2''' Device Two: Projector Tracker ===
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To meet these design goals, we designed three microfluidic chips: the Selection Chip to select worms of appropriate sizes, the Gaussian Plate to monitor changes in the worm’s group behavior, and the Immobilization Plate to observe live neuron activities without anesthetization. (Fig.1)
  
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Here is a more fantastic and powerful tool with a LCD Projector we design.
 
  
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==== '''2.2.1''' Basic mechanical and optics ====
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{{SUSTech_Image_Center_fill-width | filename=T--SUSTech_Shenzhen--Microfluidics--fig1overview.png |width=1000px| caption=<B>Fig. 1 Three microfluidic systems in our experiment. A) </B>Design of the Selection Chip and the Gaussian Chip.<B> B) </B>The Selection Chip and the Gaussian Chip, fabricated on the same substrate <B>C)</B>  Design of the Immobilization Chip.<B> D)</B> The Immobilization Chip.}}
  
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We need 395nm light to activate Calcium indicator protein GEM-GECO by Lumencor LED Illuminator. Then CoChR and Chrimson are activated by blue light and red light from LCD projector. LCD projector and LED Illuminator are merged by a double LH Adapter contained a semi-transparent mirror. Double LH Adapter connect to entrance of light in microscope. So we can use these two light source in the same time.
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<html><a target="_black" href="https://2017.igem.org/Team:SUSTech_Shenzhen/Hardware/Microfluidics" class="btn btn-default"><i class="ion-arrow-right-c"></i> Detailed Microfluidics</a></html>
  
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{{SUSTech_Image_Center_8 | filename=T--SUSTech_Shenzhen--IMG_20170320_233120_HDR.jpg|caption= Apparatus to merge projector and microscope. }}
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= Light Modulator =
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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 attempts to modulate the spatio-temporal pattern in an '''elegant''' and '''effective''' way. We constructed projector light source and modulated mercury lamp. Just let us start to play with light.
  
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We use 395nm light to activate calcium indicator protein GEM-GECO by Lumencor LED Illuminator. Then CoChR and Chrimson are activated by blue light and red light from LCD projector. LCD projector and LED Illuminator are merged by a double LH Adapter contained a semi-transparent mirror, which connect to microscope. So we can use these two light source in the same time. To achieve the aim, we add additional filter to purify the red light and blue light and replace new lens to adjust the focus distance(Fig. 2).
  
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{{SUSTech_Image | filename=T--SUSTech_Shenzhen--projectorintomicroscope.jpg|width=200px| caption=We project a movie on the hand.}}
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{{SUSTech_Image_Center_fill-width | filename=T--SUSTech_Shenzhen--SetofFilter.png| width=10000px | caption=Fig. 2 A) Spectra of filters 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}}
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We choose projector as red and blue light source, because we can activate single cell or ''<i>C. elegans</i>'' by light of adjustable color and intensity. Because the focus distance of origin lens in projector too short for our microscopy(Nikon Ti-E), a longer focus distance lens is replaced. We install a new lens into projector. Smaller the image of projector, and put image into microscope.
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Protein are sensitive to the wavelength of light, it necessary to purify light of the projector. We buy and replace with new  filter [https://www.chroma.com/products/parts/et480-20x Chroma ET480/20X] and [https://www.chroma.com/products/parts/et630-20x Chroma ET630/20X], both are fixed inside projector. Di-mirror [https://www.chroma.com/products/parts/89402bs 89402bs] and emission filter [https://www.chroma.com/products/parts/89402m 89402m] are been installed in Microscope filter wheel.
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{{SUSTech_Image_Center8 | filename=T--SUSTech_Shenzhen--SetofFilter.png| caption=Spectra of filter and mirrors are used in our system. The ET630/20X is for Chrimson, and ET480/20x is for CoChR. Both these are installed inside projector, and Di-mirror and emission filter are installed inside microscope}}
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We try develop a powerful and hackable open source software suite called ''ColorMapping'' to track and activate multi ''<i>C. elegans</i>'' or cell independently in one view(Fig. 3). User can modify multi color, intensity, time, locations of light alternately. ''ColorMapping'' can be found in [https://github.com/JiangXL/ColorMapping GitHub], which still is developing.
  
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<html><h3 style="color:white">Hi, dear stranger! Nice to see you!!!</h3></html>
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{{SUSTech_Image_Center_fill-width | filename=T--SUSTech_Shenzhen--LightModulator_Software.jpg |width=10003px | caption='''Fig. 3 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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<html><h4>2.2.2 Control Software</h4></html>
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{{SUSTech_Image | filename=T--SUSTech_Shenzhen--Stiumaltion_slide.png|width=200px| caption=We project a movie on the hand.}}
 
  
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Software is most flexible part. A very easy knack is to use slide(Demo slide[https://static.igem.org/mediawiki/2017/f/f1/T--SUSTech_Shenzhen--slidestimulation.zip]), such as LibreOffice[https://www.libreoffice.org/en](Test on 5.4.2.2.0+ in Arch Linux) or Microsoft Office. The image and time pattern  is stetted in slide, including color, intensity, pulse time etc.
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For training ''C. elegans'', we develop a simple and effective device to output pulse of certain wavelength of light. On time and off time of pulse is custom by chip. Wavelength of light is changed by replacing filter inside beam expander.(Fig. 4)
  
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We try develop a more challenged and hackable open source software suit called ''ColorMapping'' to track and activate multi ''<i>C. elegans</i>s'' or cell independently in one eye-filed. User can modify multi color, intensity, time, locations of light alternately in GUI. ''ColorMapping'' can be found in GitHub[https://github.com/JiangXL/ColorMapping], which still is developing.　''ColorMapping'' contains camera part, projector part, user&calculation part. More detain can be found in GitHub Document and PDF[].
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{{SUSTech_Image_Center_fill-width | filename=T--SUSTech_Shenzhen--DSCF2143.jpg |width=1000px| caption='''Fig. 4 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 connect to stereoscope}}
  
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<html><a target="_black" href="https://2017.igem.org/Team:SUSTech_Shenzhen/Hardware/Light" class="btn btn-default"><i class="ion-arrow-right-c"></i> Detailed Light Modulator</a></html>
  
  

Latest revision as of 16:51, 14 December 2017

Team SUSTC-Shenzhen


Microfluidics

In our experiment, we want to study the neural network activity and behavioral response of Caenorhabditis elegans under light stimuli of specific wavelengths. Thus, we need to design an accurate and user-friendly platform for studying the collective behavior of worms with high throughput as well as live neuron-level observations under natural conditions.


To meet these design goals, we designed three microfluidic chips: the Selection Chip to select worms of appropriate sizes, the Gaussian Plate to monitor changes in the worm’s group behavior, and the Immobilization Plate to observe live neuron activities without anesthetization. (Fig.1)


T--SUSTech Shenzhen--Microfluidics--fig1overview.png
Fig. 1 Three microfluidic systems in our experiment. A) Design of the Selection Chip and the Gaussian Chip. B) The Selection Chip and the Gaussian Chip, fabricated on the same substrate C) Design of the Immobilization Chip. D) The Immobilization Chip.

Detailed Microfluidics

Light Modulator

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 attempts to modulate the spatio-temporal pattern in an elegant and effective way. We constructed projector light source and modulated mercury lamp. Just let us start to play with light.

We use 395nm light to activate calcium indicator protein GEM-GECO by Lumencor LED Illuminator. Then CoChR and Chrimson are activated by blue light and red light from LCD projector. LCD projector and LED Illuminator are merged by a double LH Adapter contained a semi-transparent mirror, which connect to microscope. So we can use these two light source in the same time. To achieve the aim, we add additional filter to purify the red light and blue light and replace new lens to adjust the focus distance(Fig. 2).

T--SUSTech Shenzhen--SetofFilter.png
Fig. 2 A) Spectra of filters 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

We try develop a powerful and hackable open source software suite called ColorMapping to track and activate multi C. elegans or cell independently in one view(Fig. 3). User can modify multi color, intensity, time, locations of light alternately. ColorMapping can be found in GitHub, which still is developing.

T--SUSTech Shenzhen--LightModulator Software.jpg
Fig. 3 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.


For training C. elegans, we develop a simple and effective device to output pulse of certain wavelength of light. On time and off time of pulse is custom by chip. Wavelength of light is changed by replacing filter inside beam expander.(Fig. 4)

T--SUSTech Shenzhen--DSCF2143.jpg
Fig. 4 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 connect to stereoscope

Detailed Light Modulator



Made by from the elegans.Inc in SUSTech_Shenzhen.

Licensed under CC BY 4.0.

  • ©2017 SUSTech_Shenzhen