Difference between revisions of "Team:TU Darmstadt/tech/software"
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can be easily accomplished by choosing the panel ‘Hologram’. The single settings provided will be further explained | 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 from point sources only. | in the section ‘controls’. The algorithm used for reconstruction is applicable for light coming from point sources only. | ||
| − | <img src="https://static.igem.org/mediawiki/2017/f/f1/T--TU_Darmstadt--background3.png" alt="A reference image for a laser system." style="width=3% | + | <img src="https://static.igem.org/mediawiki/2017/f/f1/T--TU_Darmstadt--background3.png" alt="A reference image for a laser system." style="width=3%;"> |
| − | <img src="https://static.igem.org/mediawiki/2017/0/09/T--TU_Darmstadt--wrongsample.png" alt="A raw hologram on the background." style="width=3% | + | <img src="https://static.igem.org/mediawiki/2017/0/09/T--TU_Darmstadt--wrongsample.png" alt="A raw hologram on the background." style="width=3%;"> |
| − | <img src="https://static.igem.org/mediawiki/2017/e/e4/T--TU_Darmstadt--hologram.png" alt="A reconstructed hologram with HoloPyGuy." style="width=3% | + | <img src="https://static.igem.org/mediawiki/2017/e/e4/T--TU_Darmstadt--hologram.png" alt="A reconstructed hologram with HoloPyGuy." style="width=3%;"> |
</p> | </p> | ||
Revision as of 09:23, 14 October 2017
ChiTUcare
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 employ 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 is 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 from point sources only.
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
