Software HoloPyGuy

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. 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
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

That should set up the production branch of HoloPy. For Windows, the installation process is quite similar. Install conda for python 3, then run the following commands in the anaconda prompt:
Windows 1
Windows 2
Windows 3
Windows 4

References

2

[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, Nature America, DOI:10.1038/nmeth.2114
[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: 15/10/17

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