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JeroenDoornbos committed Oct 11, 2024
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Expand Up @@ -8,7 +8,7 @@ @book{goodman2015statistical

@article{Piestun2012,
abstract = {We introduce genetic algorithms (GA) for wavefront control to focus light through highly scattering media. We theoretically and experimentally compare GAs to existing phase control algorithms and show that GAs are particularly advantageous in low signal-to-noise environments.},
author = {Rafael Piestun and Albert N. Brown and Antonio M. Caravaca-Aguirre and Donald B. Conkey},
author = {Rafael Piestun et al.},
doi = {10.1364/OE.20.004840},
issn = {1094-4087},
issue = {5},
Expand Down Expand Up @@ -130,7 +130,8 @@ @book{zandonellaMassiddaOpenScience2022

@article{cox2023model,
title = {Model-based aberration corrected microscopy inside a glass tube},
author = {Cox, DWS and Knop, T and Ivo M. Vellekoop},
author = {Daniël W.S. Cox and Ivo M. Vellekoop},
doi = {10.4121/118c6472-dfc4-419b-ba0f-5d2baba77748}
journal = {arXiv preprint arXiv:2311.13363},
year = {2023}
}
Expand All @@ -143,7 +144,7 @@ @misc{harvesters

@article{osnabrugge2017generalized,
title = {Generalized optical memory effect},
author = {Osnabrugge, Gerwin and Horstmeyer, Roarke and Papadopoulos, Ioannis N and Judkewitz, Benjamin and Ivo M. Vellekoop},
author = {Gerwin Osnabrugge et al.},
journal = {Optica},
volume = {4},
number = {8},
Expand Down Expand Up @@ -196,7 +197,7 @@ @article{astropy

@article{Thompson2016,
abstract = {Spontaneous Raman scattering is a powerful tool for chemical sensing and imaging but suffers from a weak signal. In this Letter, we present an application of adaptive optics to enhance the Raman scattering signal detected through a turbid, optically thick material. This technique utilizes recent advances in wavefront shaping techniques for focusing light through a turbid media and applies them to chemical detection to achieve a signal enhancement with little sacrifice to the overall simplicity of the experimental setup. With this technique, we demonstrate an enhancement in the Raman signal from titanium dioxide particles through a highly scattering material. This technique may pave the way to label-free tracking using the optical memory effect.},
author = {Jonathan V. Thompson and Graham A. Throckmorton and Brett H. Hokr and Vladislav V. Yakovlev},
author = {Jonathan V. Thompson et al.},
doi = {10.1364/OL.41.001769},
issn = {1539-4794},
issue = {8},
Expand All @@ -214,7 +215,7 @@ @article{Thompson2016

@article{vellekoop2008demixing,
title = {Demixing light paths inside disordered metamaterials},
author = {Ivo M. Vellekoop and Van Putten, EG and Lagendijk, A and Mosk, AP},
author = {Ivo M. Vellekoop et al.},
journal = {Optics express},
volume = {16},
number = {1},
Expand Down Expand Up @@ -307,7 +308,7 @@ @article{Ishimaru1978

@article{Aoyagi2015,
abstract = {Elucidation of neural circuit functions requires visualization of the fine structure of neurons in the inner regions of thick brain specimens. However, the tissue penetration depth of laser scanning microscopy is limited by light scattering and/or absorption by the tissue. Recently, several optical clearing reagents have been proposed for visualization in fixed specimens. However, they require complicated protocols or long treatment times. Here we report the effects of 2,2′-thiodiethanol (TDE) solutions as an optical clearing reagent for fixed mouse brains expressing a yellow fluorescent protein. Immersion of fixed brains in TDE solutions rapidly (within 30 min in the case of 400-μm-thick fixed brain slices) increased their transparency and enhanced the penetration depth in both confocal and two-photon microscopy. In addition, we succeeded in visualizing dendritic spines along single dendrites at deep positions in fixed thick brain slices. These results suggest that our proposed protocol using TDE solution is a rapid and useful method for optical clearing of fixed specimens expressing fluorescent proteins.},
author = {Yuka Aoyagi and Ryosuke Kawakami and Hisayuki Osanai and Terumasa Hibi and Tomomi Nemoto},
author = {Yuka Aoyagi et al.},
doi = {10.1371/journal.pone.0116280},
issn = {19326203},
issue = {1},
Expand All @@ -331,7 +332,7 @@ @article{ploschner2015seeing

@article{salter2014exploring,
title = {Exploring the depth range for three-dimensional laser machining with aberration correction},
author = {Salter, PS and Baum, M and Alexeev, I and Schmidt, M and Booth, MJ},
author = {P.S. Salter et al.},
journal = {Optics express},
volume = {22},
number = {15},
Expand Down Expand Up @@ -427,7 +428,7 @@ @article{Streich2021

@article{Liew2016,
abstract = {A fundamental issue that limits the efficiency of many photoelectrochemical systems is that the photon absorption length is typically much longer than the electron diffusion length. Various photon management schemes have been developed to enhance light absorption; one simple approach is to use randomly scattering media to enable broadband and wide-angle enhancement. However, such systems are often opaque, making it difficult to probe photoinduced processes. Here we use wave interference effects to modify the spatial distribution of light inside a highly scattering dye-sensitized solar cell to control photon absorption in a space-dependent manner. By shaping the incident wavefront of a laser beam, we enhance or suppress photocurrent by increasing or decreasing light concentration on the front side of the mesoporous photoanode where the collection efficiency of photoelectrons is maximal. Enhanced light absorption is achieved by reducing reflection through the open boundary of the photoanode via destructive interference, leading to a factor of 2 increase in photocurrent. This approach opens the door to probing and manipulating photoelectrochemical processes in specific regions inside nominally opaque media.},
author = {Seng Fatt Liew and Sébastien M. Popoff and Stafford W. Sheehan and Arthur Goetschy and Charles A. Schmuttenmaer and A. Douglas Stone and Hui Cao},
author = {Seng Fatt Liew et al.},
doi = {10.1021/ACSPHOTONICS.5B00642},
issn = {2330-4022},
issue = {3},
Expand Down Expand Up @@ -459,7 +460,7 @@ @article{Anderson2016

@article{micromanager,
title = {Advanced methods of microscope control using $\mu$Manager software},
author = {Edelstein, Arthur D and Tsuchida, Mark A and Amodaj, Nenad and Pinkard, Henry and Vale, Ronald D and Stuurman, Nico},
author = {Arthur D. Edelstein et al.},
journal = {Journal of biological methods},
volume = {1},
number = {2},
Expand All @@ -486,7 +487,7 @@ @misc{openwfsdocumentation

@article{Anderson2024,
abstract = {We have developed a modular graphical user interface (GUI)-based program for use in genetic algorithm-based feedback-assisted wavefront shaping. The program uses a class-based structure to separate out the universal modules (e.g. GUI, multithreading, optimization algorithms) and hardware-specific modules (e.g. code for different SLMs and cameras). This modular design makes the program easily adaptable to a wide range of lab equipment, while providing easy access to a GUI, multithreading, and three optimization algorithms (phase-stepping, simple genetic, and microgenetic).},
author = {Benjamin R. Anderson and Andrew O’Kins and Kostiantyn Makrasnov and Rebecca Udby and Patrick Price and Hergen Eilers},
author = {Benjamin R. Anderson et al.},
doi = {10.1088/2515-7647/AD6ED3},
issn = {2515-7647},
issue = {4},
Expand All @@ -503,7 +504,7 @@ @article{Anderson2024

@article{Bachelard2014,
abstract = {A laser is not necessarily a sophisticated device: pumping an amplifying medium randomly filled with scatterers makes a perfectly viable â ̃ random laserâ ™. The absence of mirrors greatly simplifies laser design, but control over the emission wavelength and directionality is lost, seriously hindering prospects for this otherwise simple laser. Recently, we proposed an approach to tame random lasers, inspired by coherent light control in complex media. Here, we implement this method in an optofluidic random laser where modes are spatially extended and overlap, making individual mode selection impossible, a priori. We show experimentally that control over laser emission can be regained even in this extreme case. By actively shaping the optical pump within the random laser, single-mode operation at any selected wavelength is achieved with spectral selectivity down to 0.06 nm and more than 10 dB side-lobe rejection. This method paves the way towards versatile tunable and controlled random lasers as well as the taming of other laser sources. © 2014 Macmillan Publishers Limited. All rights reserved.},
author = {Nicolas Bachelard and Sylvain Gigan and Xavier Noblin and Patrick Sebbah},
author = {Nicolas Bachelard et al.},
doi = {10.1038/nphys2939},
issn = {17452481},
issue = {6},
Expand All @@ -519,7 +520,7 @@ @article{Bachelard2014

@article{Park2012,
abstract = {We demonstrate controlled wavelength-dependent light focusing through turbid media using wavefront shaping. Due to the dispersion caused by multiple light scattering, light propagation through turbid media can be independently controlled between different wavelengths. Foci with various wavelengths can be generated by applying different optimized wavefronts to a highly scattering layer. Given the linearity of the transmission matrix, multiple foci with different wavelengths can also be simultaneously constructed.},
author = {Jung-Hoon Park and ChungHyun Park and YongKeun Park and Hyunseung Yu and Yong-Hoon Cho},
author = {Jung-Hoon Park et al.},
doi = {10.1364/OL.37.003261},
issn = {1539-4794},
issue = {15},
Expand All @@ -536,7 +537,7 @@ @article{Park2012


@article{Pinkard2021,
author = {Henry Pinkard and Nico Stuurman and Ivan E Ivanov and Nicholas M Anthony and Wei Ouyang and Bin Li and Bin Yang and Mark A Tsuchida and Bryant Chhun and Grace Zhang and Ryan Mei and Michael Anderson and Douglas P Shepherd and Ian Hunt-Isaak and Raymond L Dunn and Wiebke Jahr and Saul Kato and Loïc A Royer and Jay R Thiagarajah and Kevin W Eliceiri and Emma Lundberg and Shalin B Mehta and Laura Waller},
author = {Henry Pinkard et al.},
journal = {Nature Methods},
pages = {226-228},
title = {Pycro-Manager: open-source software for customized and reproducible microscope control},
Expand All @@ -545,7 +546,7 @@ @article{Pinkard2021
}

@article{Thendiyammal2020,
author = {Abhilash Thendiyammal and Gerwin Osnabrugge and Tom Knop and Ivo M. Vellekoop},
author = {Abhilash Thendiyammal et al.},
journal = {Opt. Lett.},
keywords = {Inhomogeneous optical media; Light scattering; Multiphoton microscopy; Optical coherence tomography; Refractive index; Turbid media imaging},
number = {18},
Expand All @@ -560,7 +561,7 @@ @article{Thendiyammal2020
}

@ARTICLE{Astropy2022,
author = {Astropy Collaboration et al},
author = {Astropy Collaboration et al.},
title = "{The Astropy Project: Sustaining and Growing a Community-oriented Open-source Project and the Latest Major Release (v5.0) of the Core Package}",
journal = {The Astrophysical Journal},
keywords = {Astronomy software, Open source software, Astronomy data analysis, 1855, 1866, 1858, Astrophysics - Instrumentation and Methods for Astrophysics},
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