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

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<li><a href="https://2017.igem.org/Team:TU_Darmstadt/project">Project</a></li>
 
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<h2>Software HoloPyGuy</h2>
 
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<p>Abstract: Faucibus sed lobortis aliquam lorem blandit. Lorem eu nunc metus col. Commodo id in arcu ante lorem ipsum sed accumsan erat praesent faucibus commodo ac mi lacus. Adipiscing mi ac commodo. Vis aliquet tortor ultricies non ante erat nunc integer eu ante ornare amet commetus vestibulum blandit integer in curae ac faucibus integer non. Adipiscing cubilia elementum.</p>
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<p>Here, we present an universal software solution which we, the team iGEM TU Darmstadt, created for digital inline holographic microscopy (DHIM).
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<h3>header h3</h3>
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    We therefore employe the open-source framework <b>Holopy</b> and extended the existing solution with a graphical user interface.
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<p>Abstract: Faucibus sed lobortis aliquam lorem blandit. Lorem eu nunc metus col. Commodo id in arcu ante lorem ipsum sed accumsan erat praesent faucibus commodo ac mi lacus. Adipiscing mi ac commodo. Vis aliquet tortor ultricies non ante erat nunc integer eu ante ornare amet commetus vestibulum blandit integer in curae ac faucibus integer non. Adipiscing cubilia elementum.</p>
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    The resulting software includes the connection to a raspberry pi cam as well as a control element for a commonly used blue-ray laser.
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    The graphical user interface relies on the <b>Qt5</b> framework and iss written in <b>Python</b>. The solution
 +
    aims to be applicable for self-made DIHM and an ‘easy-to-use‘ hologram reconstruction suite. The project is hosted on <b>GitHub</b> under <b>MIT License</b>
 +
    and is also available for download. A complete user manual is provided in the following section.
 +
</p>
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<h2>HoloPyGuy - an Introduction</h2>
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<p>First, a reference picture, taken without a sample, needs to be provided in order to analyze a hologram. These reference pictures can be imported by choosing the panel ‘Open Background’.
 +
Several background pictures, which are turned into one averaged hologram, is subtracted from the sample hologram, which can
 +
be imported via the panel ‘Load Sample’.
 +
A dark field image can be generated by taking a picture without laser light if you are concerned about residual light in your setup, but it is not obligatory for each setup. The settings for
 +
reconstruction are controlled using the Boxes on the left. Reconstructing a hologram
 +
can be easily accomplished by choosing the panel ‘Hologram’.  The single settings provided will be further explained
 +
in the section ‘controls’. The algorithm used for reconstruction is applicable for light coming frompoint sources only. ----------include pictures----------hopefully self captured----------and
 +
analyzed</p>
 +
            <h3>Settings</h3>
 +
            All lengths are internal converted to meters. The preset values are corresponding to
 +
our DIHM setup.
 +
 
 +
            <table style = "width:100%">
 +
        <tr>
 +
            <td>Parameters</td>
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            <td>Description</td>
 +
        </tr>
 +
        <tr>
 +
            <td>Distance</td>
 +
            <td>The distance between cam to light source in mm</td>
 +
        </tr>
 +
        <tr>
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            <td>Z min</td>
 +
            <td>Smallest distance from camera to calculate wavefronts</td>
 +
        </tr>
 +
        <tr>
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            <td>Z max</td>
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            <td>Greatest distance from camera to object of interest</td>
 +
        </tr>
 +
        <tr>
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            <td>Z steps</td>
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            <td>Number of calculate distances between Z min and Z max</td>
 +
        </tr>
 +
        <tr>
 +
            <td>Pixel out</td>
 +
            <td>Size of squared hologram reconstruction. Decrease for smaller resolution but shorter computational time</td>
 +
        </tr>
 +
        <tr>
 +
            <td>Magnification</td>
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            <td>Specifies the magnification on the output picture. Higher magnifications means higher computational costs</td>
 +
        </tr>
 +
        <tr>
 +
            <td>Wavelength</td>
 +
            <td>Wavelength of the used light in nm. Blue is 480 nm</td>
 +
        </tr>
 +
        <tr>
 +
            <td>Spacing</td>
 +
            <td>Distance between the center of two pixels. We show how to calculate it for our photosensor.</td>
 +
        </tr>
 +
    </table>
 +
 
 +
<h3>Download and further documentation</h3>
 +
We provide the entire software as it is. A short installation manual for python exists.
 +
References
 
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Revision as of 18:43, 13 October 2017

MainPage

Software HoloPyGuy

Here, we present an universal software solution which we, the team iGEM TU Darmstadt, created for digital inline holographic microscopy (DHIM). We therefore employe the open-source framework Holopy and extended the existing solution with a graphical user interface. The resulting software includes the connection to a raspberry pi cam as well as a control element for a commonly used blue-ray laser. The graphical user interface relies on the Qt5 framework and iss written in Python. The solution aims to be applicable for self-made DIHM and an ‘easy-to-use‘ hologram reconstruction suite. The project is hosted on GitHub under MIT License and is also available for download. A complete user manual is provided in the following section.

HoloPyGuy - an Introduction

First, a reference picture, taken without a sample, needs to be provided in order to analyze a hologram. These reference pictures can be imported by choosing the panel ‘Open Background’. Several background pictures, which are turned into one averaged hologram, is subtracted from the sample hologram, which can be imported via the panel ‘Load Sample’. A dark field image can be generated by taking a picture without laser light if you are concerned about residual light in your setup, but it is not obligatory for each setup. The settings for reconstruction are controlled using the Boxes on the left. Reconstructing a hologram can be easily accomplished by choosing the panel ‘Hologram’. The single settings provided will be further explained in the section ‘controls’. The algorithm used for reconstruction is applicable for light coming frompoint sources only. ----------include pictures----------hopefully self captured----------and analyzed

Settings

All lengths are internal converted to meters. The preset values are corresponding to our DIHM setup.
Parameters Description
Distance The distance between cam to light source in mm
Z min Smallest distance from camera to calculate wavefronts
Z max Greatest distance from camera to object of interest
Z steps Number of calculate distances between Z min and Z max
Pixel out Size of squared hologram reconstruction. Decrease for smaller resolution but shorter computational time
Magnification Specifies the magnification on the output picture. Higher magnifications means higher computational costs
Wavelength Wavelength of the used light in nm. Blue is 480 nm
Spacing Distance between the center of two pixels. We show how to calculate it for our photosensor.

Download and further documentation

We provide the entire software as it is. A short installation manual for python exists. References