Improved resolution in fiber bundle inline holographic microscopy using multiple illumination sources : Data and Code

This repository contains data and code underpinning the paper:<b><i>Improved resolution in fiber bundle inline holographic microscopy using multiple illumination sources</i></b>Michael R. Hughes and Callum McCall, School of Physics and Astronomy, University of Kent.Please see the paper for a full description of the data and send questions or comments to [e-mail], or visit http://research.kent.ac.uk/applied-optics/hughesDatasetsRaw data is in the <i>'data'</i> folder. All data files are 8 bit tifs. Please see the paper for detailed descriptions of the optical setup.<b>illuminator :</b> Images of the tip of the multi-fibre illuminator, with each LED turned on in turn, as well as a combined images to show the locations of all the fibres.<b>raw :</b> An example raw hologram of a USAF resolution target and a zoomed in section.<b>usaf_shifted :</b> Holograms of a USAF resolution target, with the target shifted using a translation stage between each. The numbered folders correspond to different bundle-target distances. There is also a single background image, acquired through a region of the target with no line-patterns.<b>usaf_probe, paramecium, lillium :</b> Holograms of a USAF resolution target, slide mounted paramecium and slide mounted lillium anther, all using the multifibre illuminator. Shifted holograms were created by sequentially illuminating through each fibre in the multi-fibre illuminator. The numbered folders correspond to different bundle-target distances. The 'back' folder contains background images (i.e. with no sample). Within each sub-folder there are a set of images, each acquired with a different LED turned on in sequence. Most datasets contains more than one complete cycle of 7 LED images plus a blank image with all LEDs turned off (used to identify where we are in the cycle). The 'back' folders contain a set of holograms acquired for a region of the target with no line patterns visible, using the same sequence of LEDs.<b>schematic :</b> Contains inkscape SVG files for system schematic figure.CodePython code to process the raw data and generate the figures from the paper is in the <i>'code'</i> folder.The following files are used to generate individual figures:usaf_probe.pyusaf_target_shifted.pyusaf_target_shifted_vary_n.pylillium anther.pydemonstrate_shift_errors.pyparamecium_compare_methods.pyor run <i>generate_all_figures.py</i> to run all 6 files. Output figures appear in the <i>'figures'</i> folder and other output images in the <i>'results'</i> folder.Additionally the following files are present:sr_helpers.py contains functions to simplify the processing.context.py is called by all files to allow paths to be set if needed, by default this is not needed and the file does nothing.fig_maker.py contains functions to help layout the paper figures.The <i>'pybundle' </i>folder contains archived source of the PyFibreBundle package.The <i>'pyholoscope'</i> folder contains archived source of the PyHoloscope package.For new applications, it is recommended to download the latest versions of PyFibreBundle and PyHoloscope to obtain bug fixes and other improvements.The code was tested under Python 3.8. The following packages are required:numpyscipymatplotlibpillowopencvFor faster execution, you may also wish to install these packages:numbacupy (if you have a compatible CPU)