We have developed algorithms to reconstruct in-line digital holograms in the framework of Inverse Problems Approaches (also called Bayesian or model-based approaches) since 2007. We propose here a MATLAB standalone application dedicated to reconstruction in Digital In-line Holographic Microscopy (DIHM).
This application provides multiple tools to simulate or reconstruct digital in-line holograms.
These tools include :
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simulation of aberrations in DIHM based on Zernike polynomials
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simulation of Lorenz-Mie models
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reconstruction of parametric Inverse Problems approach (including basic least square fit of hologram model) that are useful for experimental setup calibration and permit accurate self-focusing and aberration calibration
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regularized reconstruction based on IP
Please before using this application, read our articles that describe our methodology and the fields of applications of this tool.
Note that this app is only devoted for testing and should not be used for commercial purpose. It is coded for CPU, please ask us to have a CPU/GPU application (time processing can be devided by 10).
IPHolo was developed by the Optical Design and Image Reconstruction (ODIR) team at Laboratoire Hubert Curien (Saint-Etienne University), UMR CNRS 5516, more particularly in the framework of Dylan Brault's PhD thesis.
If you have any questions or if you want to give us a feedback, please contact corinne.fournier at univ-st-etienne.fr
Please fill in and submit the below form to download the software:
For Windows tutorial clic here
For Linux tutorial clic here
Bibliography :
D. Brault, T. Olivier, N. Faure, ... , F. Soulez, and C. Fournier. "Multispectral in-line hologram reconstruction with aberration compensation applied to Gram-stained bacteria microscopy." Scientific Reports, 2023.
D. Brault, T. Olivier, F. Soulez, S. Joshi, N. Faure, & C. Fournier, Accurate unsupervised estimation of aberrations in digital holographic microscopy for improved quantitative reconstruction. Optics Express, 2022.
D. Brault, C. Fournier, T. Olivier, N. Faure, S. Dixneuf, L. Thibon, L.Mees, and L. Denis. Automatic numerical focus plane estimation in digital holographic microscopy using calibration beads. Applied optics, 2022.
F. Momey, T. Olivier, and C. Fournier. "In-line Digital Holographic Microscopy Sample Reconstruction." Unconventional Optical Imaging for Biology, 2024.
A. Berdeu, T. Olivier, F. Momey, L. Denis, F. Pinston, N. Faure, and C. Fournier. Joint reconstruction of an in-focus image and of the background signal in in-line holographic microscopy. Optics and Lasers in Engineering, 2021.
A. Berdeu, O. Flasseur, L. Méès, L. Denis, F. Momey, T. Olivier, N. Grosjean, and C. Fournier. Reconstruction of in-line holograms : combining model-based and regularized inversion. Optics express, 2019.
F. Momey, L. Denis, T. Olivier, and C. Fournier. From fienup’s phase retrieval techniques to regularized inversion for in-line holography : tutorial. JOSA A, 2019.
F. Jolivet, F. Momey, L. Denis, L. Méès, N. Faure, N. Grosjean, F. Pinston, J-L. Marié, and C. Fournier. Regularized reconstruction of absorbing and phase objects from a single in-line hologram, application to fluid mechanics and micro-biology. Optics exp
C. Fournier, F. Jolivet, L. Denis, N. Verrier, E. Thiebaut, C. Allier, and T. Fournel. Pixel super-resolution in digital holography by regularized reconstruction. Applied Optics, 2017.
O. Flasseur, C. Fournier, N. Verrier, L. Denis, F. Jolivet, A. Cazier, and T. Lépine. Self-calibration for lensless color microscopy. Applied Optics, 2017.
N. Verrier, N. Grosjean, E. Dib, L. Méès, C. Fournier, and J.L. Marié. Improvement of the size estimation of 3d tracked droplets using digital in-line holography with joint estimation reconstruction. Measurement Science and Technology, 2016.
N. Verrier, C. Fournier, A. Cazier, and T. Fournel. Co-design of an in-line holographic
microscope with enhanced axial resolution : selective filtering digital holography. JOSA A, 2016.
N. Verrier and C. Fournier. Digital holography super-resolution for accurate three dimensional reconstruction of particle holograms. Optics Letters, 2015.
N. Verrier, C. Fournier, and T. Fournel. 3d tracking the Brownian motion of colloidal particles using digital holographic microscopy and joint reconstruction. Applied Optics, 2015.
N. Verrier, C. Fournier, L. Méès, and T. Fournel. In-line particle holography with an astigmatic beam : setup self-calibration using an "inverse problems" approach. Applied Optics, 2014.
M. Seifi, L. Denis, and C. Fournier. Fast and accurate 3d object recognition directly from digital holograms. JOSA A, 2013.
M. Seifi, C. Fournier, N. Grosjean, L. Méès, J.L. Marié, and L. Denis. Accurate 3d tracking and size measurement of evaporating droplets using in-line digital holography and “inverse problems” reconstruction approach. Optics Express, 2013.
L. Méès, N. Grosjean, D. Chareyron, J.L. Marié, M. Seifi, and C. Fournier. Evaporating droplet hologram simulation for digital in-line holography setup with divergent beam. JOSA A, 2013.
M. Seifi, C. Fournier, L. Denis, D. Chareyron, and J.L. Marié. Three-dimensional reconstruction of particle holograms : a fast and accurate multiscale approach. JOSA A, 2012.
C. Fournier, L. Denis, and T. Fournel. On the single point resolution of on-axis digital holography. JOSA A, 2010.
L. Denis, D. Lorenz, E. Thiébaut, C. Fournier, and D. Trede. Inline hologram reconstruction with sparsity constraints. Optics Letters, 2009.
F. Soulez, L. Denis, C. Fournier, E. Thiebaut, and C. Goepfert. Inverse problem approach for particle digital holography : accurate location based on local optimisation. JOSA A, 2007.
F. Soulez, L. Denis, E Thiebaut, C. Fournier, and C. Goepfert. Inverse problem approach in particle digital holography : out-of-field particle detection made possible. JOSA A, 2007
