Difference between revisions of "Team:TU Darmstadt/tech/software"
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<h3>Download and further documentation</h3> | <h3>Download and further documentation</h3> | ||
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<h4>Setting up your system for using HoloPyGuy</h4> | <h4>Setting up your system for using HoloPyGuy</h4> | ||
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To set it up for running, we follow the getting started section from holopy. If you use a unix based operating system, please run the following lines in command-line: | To set it up for running, we follow the getting started section from holopy. If you use a unix based operating system, please run the following lines in command-line: | ||
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<h4>Get a copy of HoloPyGuy</h4> | <h4>Get a copy of HoloPyGuy</h4> | ||
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Download the latest version from hologuy and extract the files | Download the latest version from hologuy and extract the files | ||
either from our GitHub repo our download the <a href="https://static.igem.org/mediawiki/2017/c/c9/T--TU_Darmstadt--holopyguy_software.zip">.zip</a> file. | either from our GitHub repo our download the <a href="https://static.igem.org/mediawiki/2017/c/c9/T--TU_Darmstadt--holopyguy_software.zip">.zip</a> file. | ||
Revision as of 15:42, 30 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 (DIHM). We therefore employed 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
Setting up your system for using HoloPyGuy
To set it up for running, we follow the getting started section from holopy. If you use a unix based operating system, please run the following lines in command-line:
sudo apt install conda
conda install -c conda-forge holopy
This should set up the production branch of HoloPy. For Windows, the installation process is quite similar. Install Anaconda3 for your OS. Be aware that if you let the box checked in the installer, Anaconda overwirtes the default python interpreter. Then, run the following commands in the anaconda prompt:
anaconda search holopy
anaconda show ralex0/holopy
conda install -c conda-forge emcee
conda install -c conda-forge h5netcdf
conda install --channel https://conda.anaconda.org/ralex0 holopy
Install hologuy requirements (a converter from QImage to NdArray)
conda install -c conda-forge qimage2ndarray
Get a copy of HoloPyGuy
Download the latest version from hologuy and extract the files
either from our GitHub repo our download the .zip file.
To get the latest version, it is recommended to check our git.
You can get a copy of our repository by installing git and run in a terminal:
git clone https://www.github.com/iGEMDarmstadt/holopyguy.git
python hologuy.py
References
| [1] | Shiraki, A., Taniguchi, Y., Shimobaba, T., Masuda, N., Ito, T. (2012) Handheld and low-cost digital
holographic microscopy.
arXiv:1211.0336 |
| [2] | Cotte, Y., Toy, F., Jourdain, P., Pavillon, N., Boss, D., Magistretti, P., Marquet, P., Depeursinge
(2013) Marker-free phase nanoscopy Nature Photonics, 7 (2):113
DOI: 10.1038/nphoton.2012.329 |
| [3] | Giuliano, C. B., Zhang, R., Wilson, L. G. (2014) Digital Inline Microscopy (DIHM) of Weakly-scattering Subjects Journal of Visualized Experiments, DOI:10.3791/50488 |
| [4] | Molaei, M., Sheng, J. (2014) Imaging bacterial 3D motion using digital inline holographic microscopy and correlation-based de-noising algorithm Optics Express, DOI: 10.1364/OE.22.032119 |
| [5] | Braat, J., Dirksen, P., Janssen, A. J. E. M. (2003) Diffractive Read-Out of Optical Discs, Optical Imaging
Springer Verlag |
| [6] | DDeng, Y., Chu, D., (2017) Coherence properties of different light sources and their effect on the image sharpness and
speckle of holographic displays, Scientific Report,
DOI: 10.1038/s41598-017-06215-x |
| [7] | Jericho, M. H., Kreuzer, H.J., (2011), Point Source Digital In-Line Holographic Microscopy, Chapter 1, Coherent Light Microscopy, Springer Series in Surface Sciences 46, 46
DOI: 10.1007/978-3-642-15813-1_1 |
| [8] | Rostykus, M., Moser, C. (2017) Compact lensless off-axis transmission digital holographic microscope, Optics Express, DOI: 10.1364/OE.25.016652 |
| [9] | Reichert, C. C., Herkommer, A., Claus, D. (2016) Das Smartphone als Mikroskop, AT-Fachverlag GmbH,
www.biophotonik.de |
| [10] | Moon, I., Daneshpanah, M., Anand, A., Javidi, B. (2011) Cell Identification Computational 3-D Holographic Microscopy, Optics & Photonics, 22 (6), |
| [11] | Greenbaum, A., Luo, W., Su, T., Göröcs, Z., Xue, L., Isikman S., Coskun, A., Mudanyali, O., Ozcan, A. (2012) Imaging
without lenses: achievments and remaining challenges of wide-field on-chip microscopy, |
| [12] | beniroquai (2017) Blog, https://beniroquai.wordpress.com/2016/01/20/holoscope-linsenloses-holographisches-mikroskop/, last visited: 10/15/2017 |
| [13] | BDan (2015) micromanipulator, Thingiverse, https://www.thingiverse.com/thing:923865/#files, last visited: 10/15/2017 |
| [14] | "Do-it-yourself" project for steering HD-DVD pickup homepage: http://www.diyouware.com/ last visited: 10/15/2017 |
| [15] | "HoloPy, a python framework for analyzing digital holographs, manoharan lab, Harvard https://github.com/manoharan-lab/holopy last visited: 10/18/2017 | [16] | "HoloPy, documentation, https://holopy.readthedocs.io/en/latest/users/index.html last visited: 10/18/2017 |
| [17] | User:Egelberg, OpticalSetupDHM, CC BY-SA 3.0 |
