[1] Backlund MP, et al. The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging. ChemPhysChem. 2014;15(4):587–99.

[2] Chandler T, et al. Spatio-angular fluorescence microscopy I. Basic theory. J Opt Soc Am A. 2019;36(8):1334–45.

[3] Camacho R, Täuber D, Scheblykin IG. Fluorescence anisotropy reloaded—emerging polarization microscopy methods for assessing chromophores’ organization and excitation energy transfer in single molecules, particles, films, and beyond. Adv Mater. 2019;31(22):1805671.

[4] Shroder DY, Lippert LG, Goldman YE. Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl Fluoresc. 2016;4(4):042004.

[5] Kress A, et al. Mapping the local organization of cell membranes using excitation-polarization-resolved confocal fluorescence microscopy. Biophys J. 2013;105(1):127–36.

[6] Vrabioiu AM, Mitchison TJ. Structural insights into yeast septin organization from polarized fluorescence microscopy. Nature. 2006;443(7110):466–9.

[7] Karedla N, et al. Simultaneous measurement of the three-dimensional orientation of excitation and emission dipoles. Phys Rev Lett. 2015;115(17):173002.

[8] Sosa H, et al. ADP-induced rocking of the kinesin motor domain revealed by single-molecule fluorescence polarization microscopy. Nat Struct Mol Biol. 2001;8(6):540–4.

[9] Backer AS, Lee MY, Moerner WE. Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements. Optica. 2016;3(6):659–66.

[10] Adamczyk AK, et al. DNA self-assembly of single molecules with deterministic position and orientation. ACS Nano. 2022;16(10):16924–31.

[11] DeMay BS, et al. Septin filaments exhibit a dynamic, paired organization that is conserved from yeast to mammals. J Cell Biol. 2011;193(6):1065–81.

[12] Kampmann M, et al. Mapping the orientation of nuclear pore proteins in living cells with polarized fluorescence microscopy. Nat Struct Mol Biol. 2011;18(6):643–9.

[13] Mehta SB, et al. Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells. Proc Natl Acad Sci USA. 2016;113(42):E6352–61.

[14] Livanec PW, Dunn RC. Single-molecule probes of lipid membrane structure. Langmuir. 2008;24(24):14066–73.

[15] Armendariz KP, et al. Single molecule probes of membrane structure: orientation of BODIPY probes in DPPC as a function of probe structure. Analyst. 2012;137(6):1402–8.

[16] Krasnowska EK, et al. Surface properties of cholesterol-containing membranes detected by Prodan fluorescence. Biochim Biophys Acta. 2001;1511(2):330–40.

[17] Zhanghao K, et al. Super-resolution dipole orientation mapping via polarization demodulation. Light Sci Appl. 2016;5(10):e16166.

[18] Zhanghao K, et al. Super-resolution fluorescence polarization microscopy. J Innov Opt Health Sci. 2018;11(01):1730002.

[19] Wang M, et al. Plasmonics meets super-resolution microscopy in biology. Micron. 2020;137:102916.

[20] Brasselet S, Alonso MA. Polarization microscopy: from ensemble structural imaging to single-molecule 3D orientation and localization microscopy. Optica. 2023;10(11):1486–510.

[21] Zhang O, et al. Resolving the three-dimensional rotational and translational dynamics of single molecules using radially and azimuthally polarized fluorescence. Nano Lett. 2022;22(3):1024–31.

[22] Dong B, et al. Deciphering nanoconfinement effects on molecular orientation and reaction intermediate by single molecule imaging. Nat Commun. 2019;10(1):4815.

[23] Lu J, et al. Single-molecule 3D orientation imaging reveals nanoscale compositional heterogeneity in lipid membranes. Angew Chem Int Ed. 2020;59(40):17572–9.

[24] Hafi N, et al. Fluorescence nanoscopy by polarization modulation and polarization angle narrowing. Nat Methods. 2014;11(5):579–84.

[25] Gould TJ, et al. Nanoscale imaging of molecular positions and anisotropies. Nat Methods. 2008;5(12):1027–30.

[26] Zhang O, et al. Six-dimensional single-molecule imaging with isotropic resolution using a multi-view reflector microscope. Nat Photon. 2023;17(2):179–86.

[27] Zhanghao K, et al. Super-resolution imaging of fluorescent dipoles via polarized structured illumination microscopy. Nat Commun. 2019;10(1):4694.

[28] Ferrand P, et al. Ultimate use of two-photon fluorescence microscopy to map orientational behavior of fluorophores. Biophys J. 2014;106(11):2330–9.

[29] Guan M, et al. Polarization modulation with optical lock-in detection reveals universal fluorescence anisotropy of subcellular structures in live cells. Light Sci Appl. 2022;11(1):4.

[30] Wang M, et al. Polarization-based super-resolution imaging of surface-enhanced Raman scattering nanoparticles with orientational information. Nanoscale. 2018;10(42):19757–65.

[31] Chen L, et al. Group-sparsity-based super-resolution dipole orientation mapping. IEEE Trans Med Imaging. 2019;38(11):2687–94.

[32] Chen L, et al. Advances of super-resolution fluorescence polarization microscopy and its applications in life sciences. Comput Struct Biotechnol J. 2020;18:2209–16.

[33] Ha JW, Marchuk K, Fang N. Focused orientation and position imaging (FOPI) of single anisotropic plasmonic nanoparticles by total internal reflection scattering microscopy. Nano Lett. 2012;12(8):4282–8.

[34] Wu T, Lu J, Lew MD. Dipole-spread-function engineering for simultaneously measuring the 3D orientations and 3D positions of fluorescent molecules. Optica. 2022;9(5):505–11.

[35] Rimoli CV, et al. 4polar-STORM polarized super-resolution imaging of actin filament organization in cells. Nat Commun. 2022;13(1):301.

[36] Beck A, Teboulle M. A fast iterative shrinkage-thresholding algorithm for linear inverse problems. SIAM J Img Sci. 2009;2(1):183–202.

[37] Bhotto MZA, Ahmad MO, Swamy MNS. An improved fast iterative shrinkage thresholding algorithm for image deblurring. SIAM J Imaging Sci. 2015;8(3):1640–57.

[38] Rao CR. Information and the accuracy attainable in the estimation of statistical parameters. In: Kotz S, Johnson NL, editors. Breakthroughs in statistics: foundations and basic theory. New York: Springer New York; 1992. p. 235–47.

[39] Pilarski S, Pokora O. On the Cramér-Rao bound applicability and the role of Fisher information in computational neuroscience. Biosystems. 2015;136:11–22.

[40] Thorsen RØ, et al. Photon efficient orientation estimation using polarization modulation in single-molecule localization microscopy. Biomed Opt Express. 2022;13(5):2835–58.

[41] Forkey JN, Quinlan ME, Goldman YE. Protein structural dynamics by single-molecule fluorescence polarization. Prog Biophys Mol Biol. 2000;74(1):1–35.

[42] Zhanghao K, et al. High-dimensional super-resolution imaging reveals heterogeneity and dynamics of subcellular lipid membranes. Nat Commun. 2020;11(1):5890.

[43] He C, et al. Polarisation optics for biomedical and clinical applications: a review. Light Sci Appl. 2021;10(1):194.

[44] Liu Y, et al. Comparison of phospholipid composition and microstructure of milk fat globules contained in human milk and infant formulae. Food Chem. 2023;415:135762.

[45] Gunther G, et al. LAURDAN since Weber: the quest for visualizing membrane heterogeneity. Acc Chem Res. 2021;54(4):976–87.

[46] Sezgin E, et al. A comparative study on fluorescent cholesterol analogs as versatile cellular reporters. J Lipid Res. 2016;57(2):299–309.

[47] Bennink ML, et al. Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1. Cytometry. 1999;36(3):200–8.10.1002/(SICI)1097-0320(19990701)36:3<200::AID-CYTO9>3.0.CO;2-T

[48] Xu J, et al. Enabling programmable dynamic DNA chemistry using small-molecule DNA binders. Nat Commun. 2023;14(1):4248.

[49] Biebricher AS, et al. The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics. Nat Commun. 2015;6(1):7304.

[50] Fogg JM, et al. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun. 2021;12(1):5683.

[51] Cloutier TE, Widom J. Spontaneous sharp bending of double-stranded DNA. Mol Cell. 2004;14(3):355–62.

[52] Yan J, Marko JF. Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys Rev Lett. 2004;93(10):108108.

[53] Wiggins PA, Phillips R, Nelson PC. Exact theory of kinkable elastic polymers. Phys Rev E. 2005;71(2):021909.

[54] Park G, Cho MK, Jung Y. Sequence-dependent kink formation in short DNA loops: theory and molecular dynamics simulations. J Chem Theory Comput. 2021;17(3):1308–17.

[55] Xu K, Babcock HP, Zhuang X. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods. 2012;9(2):185–8.

[56] Lappalainen P, et al. Biochemical and mechanical regulation of actin dynamics. Nat Rev Mol Cell Biol. 2022;23(12):836–52.

[57] Descloux A, Grußmayer KS, Radenovic A. Parameter-free image resolution estimation based on decorrelation analysis. Nat Methods. 2019;16(9):918–24.

[58] Valades Cruz CA, et al. Quantitative nanoscale imaging of orientational order in biological filaments by polarized superresolution microscopy. Proc Natl Acad Sci USA. 2016;113(7):E820–8.

[59] Anitei M, Hoflack B. Bridging membrane and cytoskeleton dynamics in the secretory and endocytic pathways. Nat Cell Biol. 2012;14(1):11–9.

[60] Oda T, Namba K, Maéda Y. Position and orientation of phalloidin in F-actin determined by X-Ray fiber diffraction analysis. Biophys J. 2005;88(4):2727–36.

[61] Gasecka A, et al. Quantitative imaging of molecular order in lipid membranes using two-photon fluorescence polarimetry. Biophys J. 2009;97(10):2854–62.

[62] Wen G, et al. Spectrum-optimized direct image reconstruction of super-resolution structured illumination microscopy. PhotoniX. 2023;4(1):19.

[63] Chen X, et al. Superresolution structured illumination microscopy reconstruction algorithms: a review. Light Sci Appl. 2023;12(1):172.

[64] Li Y, et al. High-speed autopolarization synchronization modulation three-dimensional structured illumination microscopy. Adv Photon Nexus. 2023;3(1):016001.

[65] Cao R, et al. Author Correction: Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform. Nat Methods. 2023;20(9):1437–1437.

[66] Xi P, et al. Ultra-high spatio-temporal resolution imaging with parallel acquisition-readout structured illumination microscopy (PAR-SIM). Research Square; 2023. .

[67] Chen X, et al. Self-supervised denoising for multimodal structured illumination microscopy enables long-term super-resolution live-cell imaging. PhotoniX. 2024;5(1):4.

[68] Hou Y, et al. Noise-robust, physical microscopic deconvolution algorithm enabled by multi-resolution analysis regularization. bioRxiv; 2023. .

[69] He K, Sun J, Tang X. Single image haze removal using dark channel prior. IEEE Trans Pattern Anal Mach Intell. 2011;33(12):2341–53.

[70] Zhou Z, et al. Adaptive optical microscopy via virtual-imaging-assisted wavefront sensing for high-resolution tissue imaging. PhotoniX. 2022;3(1):13.

[71] Zhang C, et al. Deep tissue super-resolution imaging with adaptive optical two-photon multifocal structured illumination microscopy. PhotoniX. 2023;4(1):38.

[72] Zhang Y, et al. Multi-focus light-field microscopy for high-speed large-volume imaging. PhotoniX. 2022;3(1):30.