Difference between revisions of "Team:TU Darmstadt/tech/hardware"

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<h2>Digital Inline Holographic Microscopy - An iGEM Approach</h2>
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<h2>Digital Inline Holographic Microscopy - An iGEM Approach</h2>
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In light of the iGEM competition, the need for analyzing the 3D structures of hydrogel and E.Coli at micrometer scales has arisen. Our project aims at constructing a low cost Digital Inline Holography Microscope (DIHM). The DIHM features on its ease-of-use, lens-less inline structure, and the state-of-art reconstruction algorithms from holograms to 3D visualization with micrometer resolution. The working principle of a DIHM starts with a point laser source, emanating a spherical wave through a pinhole, illuminating the object to be observed, and forming a magnified diffraction pattern at the CCD camera, followed by reconstruction algorithms. The holograms collected by the CCD camera already contains the difference of intensity and phase shifts, compared with the reference beam from the spherical wave, thus the inline structure without the need of a lens or beam splitter. Our project uses easily accessible hardware components: an xbox 360 pickup as the laser source, DIYouware PCB board for the alignment and laser intensity control, a 1 µm pinhole, a Pi-cam and the Raspberry Pi for taking pictures, and certain 3D printed parts to assemble the microscope. The open source library Holopy is then deployed to reconstruct the 3D volumes from the holograms.
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In light of the iGEM competition, the need for analyzing the 3D structures of hydrogel and E.Coli at micrometer scales has arisen. Our project aims at constructing a low cost Digital Inline Holography Microscope (DIHM). The DIHM features on its ease-of-use, lens-less inline structure, and the state-of-art reconstruction algorithms from holograms to 3D visualization with micrometer resolution. The working principle of a DIHM starts with a point laser source, emanating a spherical wave through a pinhole, illuminating the object to be observed, and forming a magnified diffraction pattern at the CCD camera, followed by reconstruction algorithms. The holograms collected by the CCD camera already contains the difference of intensity and phase shifts, compared with the reference beam from the spherical wave, thus the inline structure without the need of a lens or beam splitter. Our project uses easily accessible hardware components: an xbox 360 pickup as the laser source, DIYouware PCB board for the alignment and laser intensity control, a 1 µm pinhole, a Pi-cam and the Raspberry Pi for taking pictures, and certain 3D printed parts to assemble the microscope. The open source library Holopy is then deployed to reconstruct the 3D volumes from the holograms.
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<h3>Achievements</h3>
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<p>It achieves!</p>
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<p>It achieves!</p>
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<p>It gets!</p>
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<h3>Get It</h3>
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<p>It gets!</p>
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<h3>Working Principle</h3>
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<p>It works!</p>
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<h3>Working Principle</h3>
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<h3>References</h3>
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<li>Holopy: <a href="python.org">HoloPy</a></li>
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                <li>Holopy: <a href="python.org">HoloPy</a></li>
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                                    <h3>References</h3>
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                                                <td id="[1]">[1]</td>
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                                                <td>Samain, E., Drouillard, S., Heyraud, A., Driguez, H., and Geremia, R. A. (1997) Gram-scale synthesis of recombinant chitooligosaccharides in <i>Escherichia coli</i>. <i>Carbohydrate Research</i>, 302, 35 – 42
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                                                <br>DOI: 10.1016/S0008-6215(97)00107-9</td>
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                                                <td id="[2]">[2]</td>
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                                                <td>Kurita, K. (2006) Chitin and Chitosan: Functional Biopolymers from Marine Crustaceans. <i>Marine Biotechnology</i>, 8, 203 – 226
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                                                <br>DOI: 10.1007/s10126-005-0097-5</td>
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                                                <td id="[3]">[3]</td>
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                                                <td>Knight, T. (2003) Idempotent Vector Design for Standard Assembly of Biobricks. <i>MIT Artificial Intellignece Laboratory</i> </td>
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                                                <td id="[4]">[4]</td>
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                                                <td>Dutta, P. K., Dutta, J., and Tripathi, V. S. (2004) Chitin and Chitosan: Chemistry, properties and applications. <i>Journal of Scientific &amp; Industrial Research</i>, 63, 20 – 31  </td>
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                                                <td id="[5]">[5]</td>
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                                                <td> Kumar, M. N. V. R. (2000) A review of chitin and chitosan applications. <i>Reactive &amp; Functional Polymers</i>, 46, 1 – 27
 +
                                                <br>DOI: 10.1016/S1381-5148(00)00038-9</td>
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                                                <td id="[6]">[6]</td>
 +
                                                <td>Debellé, F., Rosenberg, C., and Dénarié, J. (1992) The <i>Rhizobium, Bradyrhizobium</i>, and <i>Azorhizobium</i> NodC proteins are homologous to yeast chitin synthases. <i>Molecular Plant-Microbe Interactions</i>, 5, 443 – 446
 +
                                                <br>PMID: 1472721</td>
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                                                <td id="[7]">[7]</td>
 +
                                                <td>Long, S. R. (1996) <i>Rhizobium</i> Symbiosis: Nod Factors in Perspective. <i>The Plant Cell</i>, 8, 1885 – 1898
 +
                                                <br>DOI: 10.1105/tpc.8.10.1885</td>
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                                                <td id="[8]">[8]</td>
 +
                                                <td>Barny, M. A., and Downie, J. A. (1993) Identification of the NodC Protein in the Inner but Not the Outer Membrane of <i>Rhizobium leguminosarum</i>. <i>Molecular Plant-Microbe Interactions</i>, 6, 669 – 672</td>
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                                                <td id="[9]">[9]</td>
 +
                                                <td>Dorfmueller, H.C., Ferenbach, A. T., Borodkin, V. S., and van Aalten, D. M. F. (2014) A Structural and Biochemical Model of Processive Chitin Synthesis. <i>The Journal of Biological Chemistry</i>, 289, 23020 – 23028
 +
                                                <br>DOI: 10.1074/jbc.M114.563353</td>
 +
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                                                <td id="[10]">[10]</td>
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                                                <td>Kamst, E., van der Drift, K. M. G. M., Thomas-Oates, J. E., Lugtenberg, B. J. J., and Spaink, H. P. (1995) Mass Spectrometric Analysis of Chitin Oligosaccharides Produced by <i>Rhizobium</i> NodC Protein in <i>Escherichia coli</i>. <i>Journal of Bacteriology</i>, 177, 6282 - 6285
 +
                                                <br>DOI:  10.1128/jb.177.21.6282-6285.199</td>
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                                                <td id="[11]">[11]</td>
 +
                                                <td>Promega (2015) UDP-Glo<sup>TM</sup> Glycosyltransferase Assay, Technical Manual</td>
 +
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Revision as of 10:52, 15 October 2017

MainPage

Digital Inline Holographic Microscopy - An iGEM Approach

In light of the iGEM competition, the need for analyzing the 3D structures of hydrogel and E.Coli at micrometer scales has arisen. Our project aims at constructing a low cost Digital Inline Holography Microscope (DIHM). The DIHM features on its ease-of-use, lens-less inline structure, and the state-of-art reconstruction algorithms from holograms to 3D visualization with micrometer resolution. The working principle of a DIHM starts with a point laser source, emanating a spherical wave through a pinhole, illuminating the object to be observed, and forming a magnified diffraction pattern at the CCD camera, followed by reconstruction algorithms. The holograms collected by the CCD camera already contains the difference of intensity and phase shifts, compared with the reference beam from the spherical wave, thus the inline structure without the need of a lens or beam splitter. Our project uses easily accessible hardware components: an xbox 360 pickup as the laser source, DIYouware PCB board for the alignment and laser intensity control, a 1 µm pinhole, a Pi-cam and the Raspberry Pi for taking pictures, and certain 3D printed parts to assemble the microscope. The open source library Holopy is then deployed to reconstruct the 3D volumes from the holograms.

Achievements

It achieves!

Get It

It gets!

Working Principle

It works!

References

References

[1] Samain, E., Drouillard, S., Heyraud, A., Driguez, H., and Geremia, R. A. (1997) Gram-scale synthesis of recombinant chitooligosaccharides in Escherichia coli. Carbohydrate Research, 302, 35 – 42
DOI: 10.1016/S0008-6215(97)00107-9
[2] Kurita, K. (2006) Chitin and Chitosan: Functional Biopolymers from Marine Crustaceans. Marine Biotechnology, 8, 203 – 226
DOI: 10.1007/s10126-005-0097-5
[3] Knight, T. (2003) Idempotent Vector Design for Standard Assembly of Biobricks. MIT Artificial Intellignece Laboratory
[4] Dutta, P. K., Dutta, J., and Tripathi, V. S. (2004) Chitin and Chitosan: Chemistry, properties and applications. Journal of Scientific & Industrial Research, 63, 20 – 31
[5] Kumar, M. N. V. R. (2000) A review of chitin and chitosan applications. Reactive & Functional Polymers, 46, 1 – 27
DOI: 10.1016/S1381-5148(00)00038-9
[6] Debellé, F., Rosenberg, C., and Dénarié, J. (1992) The Rhizobium, Bradyrhizobium, and Azorhizobium NodC proteins are homologous to yeast chitin synthases. Molecular Plant-Microbe Interactions, 5, 443 – 446
PMID: 1472721
[7] Long, S. R. (1996) Rhizobium Symbiosis: Nod Factors in Perspective. The Plant Cell, 8, 1885 – 1898
DOI: 10.1105/tpc.8.10.1885
[8] Barny, M. A., and Downie, J. A. (1993) Identification of the NodC Protein in the Inner but Not the Outer Membrane of Rhizobium leguminosarum. Molecular Plant-Microbe Interactions, 6, 669 – 672
[9] Dorfmueller, H.C., Ferenbach, A. T., Borodkin, V. S., and van Aalten, D. M. F. (2014) A Structural and Biochemical Model of Processive Chitin Synthesis. The Journal of Biological Chemistry, 289, 23020 – 23028
DOI: 10.1074/jbc.M114.563353
[10] Kamst, E., van der Drift, K. M. G. M., Thomas-Oates, J. E., Lugtenberg, B. J. J., and Spaink, H. P. (1995) Mass Spectrometric Analysis of Chitin Oligosaccharides Produced by Rhizobium NodC Protein in Escherichia coli. Journal of Bacteriology, 177, 6282 - 6285
DOI: 10.1128/jb.177.21.6282-6285.199
[11] Promega (2015) UDP-GloTM Glycosyltransferase Assay, Technical Manual