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References

Every literature value, default or model in the simulator names one of these keys where it is used (data files under data/, code comments, these pages). Checked says how the citation, and where stated the values, were verified. Generated from data/references.json by tools/gen_dye_library.mjs; edit that file, not this page.

  • abramowitz1964 -- Abramowitz M, Stegun IA (eds.) (1964). Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables. National Bureau of Standards, Applied Mathematics Series 55 eq. 7.1.26, p. 299.
    Used for: the rational approximation of erf (|error| <= 1.5e-7) behind the drift swings (DriftSwing in Simulation/Drift.*). Checked: the coefficients and error bound as commonly reproduced from eq. 7.1.26, not re-read from the scan; the bound checked numerically against erf in ctest drift.
  • axelrod1981 -- Axelrod D (1981). Cell-substrate contacts illuminated by total internal reflection fluorescence. Journal of Cell Biology 89 141-145. doi:10.1083/jcb.89.1.141 (PMC2111781)
    Used for: the evanescent wave I = I0 exp(-z/d) and its decay depth d = lambda / (4 pi n2) (sin^2 theta / sin^2 theta_c - 1)^(-1/2) (eq. 1, 2), i.e. lambda / (4 pi n_s sqrt(u^2 - 1)) with the BFP position u; d diverges at the critical angle; the check value theta = 72.5 deg, n1 = 1.44, theta_c = 67.5 deg, 514.5 nm: d = 120 nm (Fig. 2, Methods). Checked: equations, the check value and the statements read from the Europe PMC full text (PMC2111781).
  • axelrod1984 -- Axelrod D, Burghardt TP, Thompson NL (1984). Total internal reflection fluorescence. Annual Review of Biophysics and Bioengineering 13 247-268. doi:10.1146/annurev.bb.13.060184.001335
    Used for: the evanescent field's components and phases at the interface for s and p polarisation (E_y for s; E_x and E_z for p, a quarter turn apart: the p field is elliptically polarised in the plane of incidence), with the phase shifts delta_s = atan(sqrt(sin^2 theta - n^2) / cos theta) and delta_p = atan(sqrt(sin^2 theta - n^2) / (n^2 cos theta)). Here: BeamFieldOf's evanescent fields, whose |E|^2 are axelrod2001's I_s and I_p. Checked: citation via PubMed (no abstract; not open access); the component amplitudes and phases are the standard evanescent-wave Fresnel results, checked here against axelrod2001's intensities (|E_y|^2 = I_s, |E_x|^2 + |E_z|^2 = I_p, ctest sim_pattern through the two-beam contrast), not read from this review's full text.
  • axelrod2001 -- Axelrod D (2001). Total internal reflection fluorescence microscopy in cell biology. Traffic 2 764-774. doi:10.1034/j.1600-0854.2001.21104.x
    Used for: objective-type TIRF through a high-NA objective; the evanescent intensities at the interface for s and p polarisation, I_s(0) = 4 cos^2 theta / (1 - n^2), I_p(0) = 4 cos^2 theta (2 sin^2 theta - n^2) / (n^4 cos^2 theta + sin^2 theta - n^2), n = n2 / n1 (relative to the incident intensity): 4 and 4 / n^2 at the critical angle. Checked: citation and abstract via PubMed (not open access); the intensity formulas are the standard Fresnel results, checked for continuity with the transmitted Fresnel coefficients at the critical angle, not read from this paper's full text.
  • balinovic2019 -- Balinovic A, Albrecht D, Endesfelder U (2019). Spectrally red-shifted fluorescent fiducial markers for optimal drift correction in localization microscopy. Journal of Physics D: Applied Physics 52 204002. doi:10.1088/1361-6463/ab0862
    Used for: fiducial markers (data/fiducials/): excitation and emission spectra of gold nanoparticles, TetraSpeck orange dye, dark red and infrared FluoSpheres and red nanodiamonds read from figures 2a-6a (CC BY 3.0); their quoted excitation and filter efficiencies (figure panels a) and brightness relative to mEos3.2-A69T / JF646-Hoechst in the same images (max-pixel histograms, figs 2d, 3b, 4b, 5e, 6d: EM gain 300, 561 nm 725 W/cm^2, 640 nm 750 W/cm^2, iXon Ultra 888, NA 1.49; Methods). Checked: citation via Crossref; figures and Methods read in the open-access article (iopscience); the curves read by eye on calibrated grid overlays (tools/fiducial_spectra/README.md).
  • bindels2017 -- Bindels DS, Haarbosch L, van Weeren L, Postma M, Wiese KE, Mastop M, Aumonier S, Gotthard G, Royant A, Hink MA, Gadella TW (2017). mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nature Methods 14 53-56. doi:10.1038/nmeth.4074
    Used for: mScarlet. Checked: citation via Europe PMC.
  • bluestein1970 -- Bluestein L (1970). A linear filtering approach to the computation of discrete Fourier transform. IEEE Transactions on Audio and Electroacoustics 18 451-455. doi:10.1109/TAU.1970.1162132
    Used for: Bluestein's algorithm (a DFT as a chirp convolution), the core of the chirp-z transform. Checked: bibliographic details from the Crossref DOI record; not re-read.
  • bohren1983 -- Bohren CF, Huffman DR (1983). Absorption and Scattering of Light by Small Particles. Wiley-VCH. doi:10.1002/9783527618156
    Used for: Mie theory: the BHMIE algorithm (appendix A: logarithmic derivative by downward recurrence, Riccati-Bessel recurrences) and the small-sphere limits (section 5.2) for the gold fiducials' cross sections (tools/fiducial_spectra/gold_mie.mjs). Checked: citation via Crossref (Wiley online edition 1998); the algorithm written from the published BHMIE structure, checked against the dipole limit and a lossless sphere in the tool.
  • bornwolf1999 -- Born M, Wolf E (1999). Principles of Optics, 7th edition. Cambridge University Press.
    Used for: Fresnel amplitude transmission coefficients t_s = 2 n1 cos theta_i / (n1 cos theta_i + n2 cos theta_t), t_p = 2 n1 cos theta_i / (n2 cos theta_i + n1 cos theta_t) (section 1.5.2); the power transmittance T = (n2 cos theta_t / n1 cos theta_i) |t|^2 (section 1.5.3: the free imager's collected light into the coverslip, excitation.js collectionRings); Snell's law; the sine condition (the BFP radius ~ n sin theta). Checked: standard textbook results, written from the formulas (not checked against the book itself).
  • catmull1974 -- Catmull E, Rom R (1974). A class of local interpolating splines. Computer Aided Geometric Design (Academic Press) 317-326. doi:10.1016/B978-0-12-079050-0.50020-5
    Used for: the Catmull-Rom cubic of the Cubic PSF placement (Renderer.PsfInterp = Cubic). Checked: bibliographic details from the Crossref DOI record; not re-read.
  • chhabra2020 -- Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK (2020). Computing the elastic mechanical properties of rod-like DNA nanostructures. Journal of Chemical Theory and Computation 16 7748-7763. doi:10.1021/acs.jctc.0c00661
    Used for: measured bending persistence lengths of origami helix bundles, summarised from the literature: 740 nm-1 um (four-helix), 1-3 um (six-helix), 3-8.2 um (eight-helix) bundles (Introduction, p. 4 of the arXiv version); oxDNA gives somewhat higher values (abstract): the range the nanorulers' persistence length is compared with. Checked: values read from the arXiv full text (2006.15029v1); journal citation from the arXiv record.
  • cnossen2021 -- Cnossen J, Cui TJ, Joo C, Smith C (2021). Drift correction in localization microscopy using entropy minimization. Optics Express 29 27961-27974. doi:10.1364/OE.426620
    Used for: sample drift as a random walk: a normal step per frame, cumulated (the drift model of Simulation/Drift.*). Checked: bibliographic details from the DOI record; the model read from the bioRxiv preprint full text (doi:10.1101/2021.03.30.437682): drift 'simulated using a cumulative normal distribution', a new offset per frame from N(0.02 nm, 4 nm^2) (Fig. 3 caption; Fig. 4); the published version not re-read.
  • cowley1957 -- Cowley JM, Moodie AF (1957). The scattering of electrons by atoms and crystals. I. A new theoretical approach. Acta Crystallographica 10 609-619. doi:10.1107/S0365110X57002194
    Used for: the multislice method (thin phase screens alternating with free-space propagation steps): the BrightField propagation through the cell slices. Checked: bibliographic details from the Crossref DOI record; not re-read.
  • dempsey2011 -- Dempsey GT, Vaughan JC, Chen KH, Bates M, Zhuang X (2011). Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nature Methods 8 1027-1036. doi:10.1038/nmeth.1768 (PMC3272503)
    Used for: dSTORM switching: detected photons per cycle, equilibrium duty cycle, switching cycles (Table 1, GLOX + 10 mM MEA) at their measurement intensities (488 nm 1.2, 561 nm 2.2, 647 nm 0.8 kW/cm^2; Methods); 405 nm activation sensitivity (Table 2); photons per cycle and duty cycle largely independent of intensity (emission, off- and on-switching linear in it; Results, Supplementary Fig. 32): the intensity scaling of dSTORM ON and dark times. Checked: Table 1 and 2 values, the intensities and the intensity-dependence statements read from the Europe PMC full text (PMC3272503).
  • dempsey2015 -- Dempsey WP, Georgieva L, Helbling PM, Sonay AY, Truong TV, Haffner M, Pantazis P (2015). In vivo single-cell labeling by confined primed conversion. Nature Methods 12 645-648. doi:10.1038/nmeth.3405
    Used for: discovery of primed conversion (Dendra2, 488 nm + 730 nm). Checked: citation and abstract via Europe PMC.
  • dultz2010 -- Dultz E, Ellenberg J (2010). Live imaging of single nuclear pores reveals unique assembly kinetics and mechanism in interphase. Journal of Cell Biology 191 15-22. doi:10.1083/jcb.201007076 (PMC2953446)
    Used for: NPC density 6.9 +/- 0.7 (early G1) to 6.4 +/- 0.8 (late G2) per um^2 in NRK cells, the same on the top and bottom surfaces (Results, Fig. 1C); 1960-2830 NPCs per nucleus; new pores appear independently of the positions of existing ones. Checked: Europe PMC full text.
  • durisic2014 -- Durisic N, Laparra-Cuervo L, Sandoval-Álvarez A, Borbely JS, Lakadamyali M (2014). Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate. Nature Methods 11 156-162. doi:10.1038/nmeth.2784
    Used for: photoactivation efficiency of mEos2/3.1/3.2, Dendra2, mMaple, PA-GFP, PA-mCherry (the fluorescent fraction of the PALM entries). Checked: citation and abstract via Europe PMC; the full text was not available, so the fractions used are estimates of the reported range.
  • frohn2001 -- Frohn JT, Knapp HF, Stemmer A (2001). Three-dimensional resolution enhancement in fluorescence microscopy by harmonic excitation. Optics Letters 26 828-830. doi:10.1364/ol.26.000828
    Used for: harmonic excitation patterns from the interference of collimated laser beams: the pattern as the squared sum of plane waves, each beam a direction in the pupil. Here: the pattern model (every beam a plane wave with the direction its BFP position gives, the intensity |sum E_j|^2). Checked: citation and abstract via PubMed (not open access).
  • fruh2021 -- Früh SM, Matti U, Spycher PR, Rubini M, Lickert S, Schlichthaerle T, Jungmann R, Vogel V, Ries J, Schoen I (2021). Site-specifically-labeled antibodies for super-resolution microscopy reveal in situ linkage errors. ACS Nano 15 12161-12170. doi:10.1021/acsnano.1c03677 (PMC8320235)
    Used for: Antibody linkage error around microtubules (STORM, Table 1): primary + secondary label shell centred 10 nm outside the 12.5 nm outer radius, maximum about 19 nm; a directly labelled primary 7.7 nm mean, 12.7 nm maximum; DNA-PAINT indirect maximum about 27-30 nm. Checked: Europe PMC full text, Table 1 and Results.
  • gibson1992 -- Gibson SF, Lanni F (1992). Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy. Journal of the Optical Society of America A 9 154-166. doi:10.1364/JOSAA.9.000154
    Used for: the Gibson-Lanni model: the aberration of an oil-immersion objective used with a sample whose index differs from the design, at depth (the pupil phase of the GibsonLanni and GibsonLanniZernike PSFs). Checked: citation and abstract via PubMed, which lists it as the corrected republication of J Opt Soc Am A 8(10):1601 (1991), doi:10.1364/JOSAA.8.001601 (Crossref); not re-read.
  • gittes1993 -- Gittes F, Mickey B, Nettleton J, Howard J (1993). Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. Journal of Cell Biology 120 923-934. doi:10.1083/jcb.120.4.923 (PMC2200075)
    Used for: persistence length of taxol-stabilized microtubules in vitro, 5,200 um: rigid over cellular dimensions (abstract), far longer than the path correlation length used for microtubules in cells. Checked: abstract via PubMed; the value also in the Europe PMC full text (PMC2200075).
  • gneiting2004 -- Gneiting T, Schlather M (2004). Stochastic models that separate fractal dimension and the Hurst effect. SIAM Review 46 269-282. doi:10.1137/S0036144501394387
    Used for: D = n + 1 - H for a self-similar (self-affine) profile or surface in n dimensions (eq. 1; D = 2 - H for an outline) and the equivalence of the small-lag correlation behaviour that sets D with the decay of the spectral density: behind the k^-(2.5-D) amplitudes of the cell outline's fractal tail. Checked: eq. (1) and the spectral-density remark read from the arXiv preprint (physics/0109031v1); the amplitude exponent H + 1/2 (power spectrum k^-(2H+1), so 2.5 - D) is worked out from it here, not quoted; journal details from the Crossref DOI record.
  • gurskaya2006 -- Gurskaya NG, Verkhusha VV, Shcheglov AS, Staroverov DB, Chepurnykh TV, Fradkov AF, Lukyanov S, Lukyanov KA (2006). Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nature Biotechnology 24 461-465. doi:10.1038/nbt1191
    Used for: Dendra2. Checked: citation via Europe PMC.
  • gustafsson2000 -- Gustafsson MG (2000). Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. Journal of Microscopy 198 82-87. doi:10.1046/j.1365-2818.2000.00710.x
    Used for: 2D structured illumination: the sample under a series of excitation patterns (a sinusoidal fringe from two interfering beams, stepped in phase and rotated), the reconstruction doubling the lateral resolution. Here: the SIM2D type (two beams, 3 phases x 3 orientations, the orientations 60 degrees apart). Checked: citation and abstract via PubMed (the paper's pattern: two beams from a grating; the 3 x 3 scheme is the standard one, not read from the full text).
  • gustafsson2008 -- Gustafsson MGL, Shao L, Carlton PM, Wang CJR, Golubovskaya IN, Cande WZ, Agard DA, Sedat JW (2008). Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophysical Journal 94 4957-4970. doi:10.1529/biophysj.107.120345
    Used for: 3D structured illumination: three mutually coherent beams (a grating's 0 and +-1 orders) interfere in the specimen to a pattern varying laterally and axially; five phase steps per orientation, three orientations, 15 raw images per plane. Here: the SIM3D type (centre + two side beams, 5 phases x 3 orientations, angle-major order). Checked: citation and abstract via PubMed (open access: PMC2397368; the five-phase, three-orientation scheme from the paper's methods).
  • heintzmann1999 -- Heintzmann R, Cremer C (1999). Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating. Proceedings of SPIE 3568 185-196. doi:10.1117/12.336833
    Used for: structured (laterally modulated) excitation from a diffraction grating, the first description of the method; background for the SIM types. Checked: citation from memory, not verified against the source (not in PubMed): treat the volume and pages as unverified.
  • hirsch2013 -- Hirsch M, Wareham RJ, Martin-Fernandez ML, Hobson MP, Rolfe DJ (2013). A stochastic model for electron multiplication charge-coupled devices -- from theory to practice. PLoS One 8 e53671. doi:10.1371/journal.pone.0053671 (PMC3561409)
    Used for: the EMCCD noise model: Poisson photoelectrons and spurious charge (dark current, clock-induced charge), the EM register as a gamma distribution (shape = input electrons, scale = EM gain), Gaussian read noise; the model gives the measured excess noise factor sqrt(2) (Results, 'The EM register model', 'The combined Poisson-Gamma distribution'). Checked: read from the Europe PMC full text (PMC3561409).
  • huang2013 -- Huang F, Hartwich TMP, Rivera-Molina FE, Lin Y, Duim WC, Long JJ, Uchil PD, Myers JR, Baird MA, Mothes W, Davidson MW, Toomre D, Bewersdorf J (2013). Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms. Nature Methods 10 653-658. doi:10.1038/nmeth.2488 (PMC3696415)
    Used for: every sCMOS pixel has its own offset, read-noise variance and gain, measured per pixel from dark and illuminated frames (Online Methods, 'Camera variance, gain and offset calibration'): the per-pixel offset, gain and read-noise maps of the sCMOS noise chain. Checked: read from the Europe PMC full text (PMC3696415); it gives no percentage for the gain spread.
  • ixon897-datasheet -- Andor Technology (Oxford Instruments) (2020). iXon Ultra 897 EMCCD camera specifications. https://andor.oxinst.com/products/ixon-emccd-cameras/ixon-ultra-897
    Used for: iXon Ultra 897 preset (EMCCD read noise, clock-induced charge, dark current at -80 C, EM gain range); QE curve via FPbase. Checked: the preset's values are typical published ones; the current iXon Ultra specification sheet (andor.oxinst.com/downloads/uploads/andor-ixon-ultra-emccd-specifications.pdf) gives for the 897: 16 um pixels, QE > 95 %, EMCCD-amplifier read noise 89 / 65 / 37 / 15 e- at 17 / 10 / 5 / 1 MHz (< 1 e- with EM gain), dark current 0.00030 e-/pixel/s at -80 C, spurious background 0.0018 events/pixel at x1000 gain and -85 C, EM gain 1-1000. The preset's 50 e-, 0.00025 e-/pixel/s and 0.005 e- CIC differ (0.00025 and 0.005 are the Ultra 888's values in the same table).
  • jarzynski2020 -- Jarzynski M, Olano M (2020). Hash Functions for GPU Rendering. Journal of Computer Graphics Techniques 9 20-38. https://jcgt.org/published/0009/03/02/
    Used for: the pcg4d hash (4 uint32 in, 4 out; introduced in the paper, Table 1 'This paper'; on the quality/speed Pareto frontier) behind every address-based random draw of the world (core/src/rng.h). Checked: title, volume, issue 3, pages 20-38 and the pcg4d statements read from the paper PDF at jcgt.org; the core's constants and steps match the commonly reproduced pcg4d listing, not compared against the paper's supplemental code.
  • johnson1972 -- Johnson PB, Christy RW (1972). Optical constants of the noble metals. Physical Review B 6 4370-4379. doi:10.1103/PhysRevB.6.4370
    Used for: optical constants n, k of gold (data/fiducials/gold_johnson_christy.json) for the gold fiducials' Mie cross sections. Checked: citation via Crossref; the table as distributed by refractiveindex.info (polyanskiy2024), not re-read from the paper.
  • jungmann2010 -- Jungmann R, Steinhauer C, Scheible M, Kuzyk A, Tinnefeld P, Simmel FC (2010). Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Letters 10 4756-4761. doi:10.1021/nl103427w
    Used for: DNA-PAINT binding kinetics (association rate of the order of 1e6 /M/s). Checked: citation via Europe PMC; the full text was not available, so the k_on used is an order-of-magnitude estimate.
  • jungmann2014 -- Jungmann R, Avendaño MS, Woehrstein JB, Dai M, Shih WM, Yin P (2014). Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nature Methods 11 313-318. doi:10.1038/nmeth.2835 (PMC4153392)
    Used for: DNA-PAINT imagers (ATTO 655, Cy3B/ATTO 542-type) in cells. Checked: citation via Europe PMC.
  • kauert2011 -- Kauert DJ, Kurth T, Liedl T, Seidel R (2011). Direct mechanical measurements reveal the material properties of three-dimensional DNA origami. Nano Letters 11 5558-5563. doi:10.1021/nl203503s
    Used for: bending rigidities of four- and six-helix origami bundles by magnetic tweezers, greatly increased over duplex DNA (abstract); one of the measurements chhabra2020 summarises. Checked: citation and abstract via PubMed; the numbers are taken from chhabra2020's summary, not read from this paper.
  • kim2015 -- Kim YJ, Kim H-D, Kim HH, Shin S-M, Kang CJ, Lee KH (2015). Fractal analysis of cell boundary ultrastructure imaged by atomic force microscopy. Animal Cells and Systems 19 161-167. doi:10.1080/19768354.2015.1037347
    Used for: contour fractal dimension of adherent cells: box counting on AFM images of cultured human epithelial MCF10A cells gives D = 1.352 +/- 0.044 for individual cells despite their varied shapes, lowered by cytochalasin D (actin-dependent): the default cellFractalDim 1.35. Checked: bibliographic details from the Crossref DOI record; D = 1.352 +/- 0.044 and the cytochalasin D result from the abstract (Korea University repository record); the full text was not open, so the box sizes and cell numbers were not read.
  • kinetix-datasheet -- Teledyne Photometrics (2024). Kinetix22 CMOS camera datasheet (Sensitivity / CMS mode). https://www.photometrics.com/products/kinetix-family/kinetix
    Used for: Kinetix22 preset noise values (read noise 1.2 e-, dark current, conversion gain) -- the adapter's defaults since 2026-09; 6.5 um pixels; QE curve via FPbase. Checked: datasheet revision 2024-10-21 read: 6.5 um pixels, peak QE 95 %; Sensitivity mode 12-bit, read noise 1.2 e-, dark current 1.03 e-/pixel/s at 0 C, conversion gain 0.25 e-/count (the preset's values); the scalar QE 0.85, the offset (100 ADU, std 0.5 ADU) and the per-pixel spreads are not on the datasheet.
  • kirshner2013 -- Kirshner H, Aguet F, Sage D, Unser M (2013). 3-D PSF fitting for fluorescence microscopy: implementation and localization application. Journal of Microscopy 249 13-25. doi:10.1111/j.1365-2818.2012.03675.x
    Used for: PSFGenerator (EPFL Biomedical Imaging Group), which computes the RichardsWolf and GibsonLanni PSFs in the adapter's JVM. Checked: citation and abstract via PubMed; listed as a reference for PSF Generator on its page (bigwww.epfl.ch/algorithms/psfgenerator).
  • kner2009 -- Kner P, Chhun BB, Griffis ER, Winoto L, Gustafsson MGL (2009). Super-resolution video microscopy of live cells by structured illumination. Nature Methods 6 339-342. doi:10.1038/nmeth.1324
    Used for: TIRF-SIM: structured illumination in the total internal reflection mode, the two beams beyond the critical angle making an evanescent fringe (100 nm resolution at up to 11 Hz). Here: a SIM type with its beams at illum-bfp > 1 (the beams' decays, the fringe's period lambda / (2 n_s u)). Checked: citation and abstract via PubMed (open access: PMC2895555).
  • lambert2019 -- Lambert TJ (2019). FPbase: a community-editable fluorescent protein database. Nature Methods 16 277-278. doi:10.1038/s41592-019-0352-8
    Used for: dye and fluorescent-protein spectra, peak wavelengths, extinction coefficients, quantum yields, lifetimes; filter and camera QE curves (data CC BY-SA 4.0). Checked: citation via Europe PMC; data fetched from the FPbase GraphQL API by tools/fetch_fpbase.mjs.
  • ma2024 -- Ma H, Chen M, Nguyen P, Liu Y (2024). Toward drift-free high-throughput nanoscopy through adaptive intersection maximization. Science Advances 10 eadm7765. doi:10.1126/sciadv.adm7765
    Used for: RMS drift of 5, 10 and 20 nm/s as test values, drift as a cumulative normal distribution (after Cnossen et al. 2021); a stable setup (optical table, active vibration isolation, constant room temperature) drifts several nm/s (Materials and Methods, Numerical simulation, 'Magnitude of drift'): the scale of SampleHolder.DriftXyNmPerSqrtSec / ZNmPerSqrtSec. Checked: the 5/10/20 nm/s values, the model and the stable-setup statement read from the Europe PMC full text (PMC11114195).
  • maeshima2006 -- Maeshima K, Yahata K, Sasaki Y, Nakatomi R, Tachibana T, Hashikawa T, Imamoto F, Imamoto N (2006). Cell-cycle-dependent dynamics of nuclear pores: pore-free islands and lamins. Journal of Cell Science 119 4442-4451. doi:10.1242/jcs.03207
    Used for: NPC density on the nuclear surface: HeLa S3 about 5 per um^2 in G1 (with pore-free islands), 8.56 +/- 0.34 per um^2 in G2 (Results, after Fig. 3); IMR90 4.85 (early G1) to 6.62 (G2) per um^2 (Fig. 7A); NPC diameter 120 nm (Introduction, citing reviews). Checked: journals.biologists.com full text (Introduction, Results); not in PMC.
  • mandelkow1986 -- Mandelkow E-M, Schultheiss R, Rapp R, Müller M, Mandelkow E (1986). On the surface lattice of microtubules: helix starts, protofilament number, seam, and handedness. Journal of Cell Biology 102 1067-1073. doi:10.1083/jcb.102.3.1067 (PMC2114131)
    Used for: the microtubule surface lattice: 4 nm monomer (8 nm dimer) repeat along a protofilament, monomers on a left-handed 3-start helix, B-lattice with a seam; neighbouring protofilaments staggered by 12 nm / 13 = 0.923 nm for 13 protofilaments (Results, Fig. 3, Fig. 4, Table I). Checked: read from the Europe PMC full text (PMC2114131).
  • mikhaylova2015 -- Mikhaylova M, Cloin BMC, Finan K, van den Berg R, Teeuw J, Kijanka MM, Sokolowski M, Katrukha EA, Maidorn M, Opazo F, Moutel S, Vantard M, Perez F, van Bergen en Henegouwen PMP, Hoogenraad CC, Ewers H, Kapitein LC (2015). Resolving bundled microtubules using anti-tubulin nanobodies. Nature Communications 6 7933. doi:10.1038/ncomms8933 (PMC4918323)
    Used for: microtubules are hollow, 25 nm in diameter; most labels widen them by 20-40 nm, anti-tubulin nanobodies less (abstract): the 12.5 nm attachment radius and the scale of the binder stalk plus linker. Checked: citation and abstract via PubMed; Europe PMC full text PMC4918323 read 2026-10-12 (nanobody ~15 kDa, ~4 nm; the dye of a direct primary ~12.5 nm from the lattice, of a VHH <2.5 nm).
  • nieves2019 -- Nieves DJ, Hilzenrat G, Tran J, Yang Z, MacRae HH, Baker MAB, Gooding JJ, Gaus K (2019). tagPAINT: covalent labelling of genetically encoded protein tags for DNA-PAINT imaging. Royal Society Open Science 6 191268. doi:10.1098/rsos.191268 (PMC6936279)
    Used for: SNAP-/HaloTag size below 5 nm, one ligand per tag (Introduction). Checked: Europe PMC full text.
  • ober2004 -- Ober RJ, Ram S, Ward ES (2004). Localization accuracy in single-molecule microscopy. Biophysical Journal 86 1185-1200. doi:10.1016/S0006-3495(04)74193-4 (PMC1303911)
    Used for: the Fisher information / Cramer-Rao bound of single-molecule localization, including pixelation and noise (the Cramer-Rao summary the adapter logs, DescribePsfCramerRao). Checked: citation and abstract via Europe PMC.
  • orcaflash4v3-technote -- Hamamatsu Photonics K.K. (2018). ORCA-Flash4.0 V3 digital CMOS camera C13440-20CU, technical note (Cat. No. SCAS0134E01). https://hep.hamamatsu.com/resources/pdf/sys/SCAS0134E_C13440-20CU_tec.pdf
    Used for: a published sCMOS photo response non-uniformity (PRNU): 0.06 % rms at 15 000 e- and 0.3 % rms at 700 e- (specifications table; Fig. 5 measures 0.06-0.11 %): the scale of the sCMOS gain spread. Checked: values read from the PDF (Cat. No. SCAS0134E01, June 2018).
  • ormo1996 -- Ormö M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ (1996). Crystal structure of the Aequorea victoria green fluorescent protein. Science 273 1392-1395. doi:10.1126/science.273.5280.1392
    Used for: GFP is an 11-stranded beta barrel with a coaxial helix; the chromophore forms from the central helix (abstract): a fluorescent protein's emitter sits inside the protein, no chemical linker. Checked: PubMed abstract (PMID 8703075).
  • polyanskiy2024 -- Polyanskiy MN (2024). Refractiveindex.info database of optical constants. Scientific Data 11 94. doi:10.1038/s41597-023-02898-2
    Used for: the Johnson & Christy gold table (main/Au/nk/Johnson.yml, CC0 1.0). Checked: citation via Crossref; data file fetched from refractiveindex.info.
  • rabiner1969 -- Rabiner LR, Schafer RW, Rader CM (1969). The chirp z-transform algorithm. IEEE Transactions on Audio and Electroacoustics 17 86-92. doi:10.1109/TAU.1969.1162034
    Used for: the chirp-z transform (a DFT on an arbitrary frequency grid by a convolution), which evaluates the GibsonLanniZernike pupil-to-image integral (Simulation/ZernikePsf.*, Simulation/ChirpZ.h). Checked: bibliographic details from the Crossref DOI record; not re-read.
  • richards1959 -- Richards B, Wolf E (1959). Electromagnetic diffraction in optical systems, II. Structure of the image field in an aplanatic system. Proceedings of the Royal Society of London A 253 358-379. doi:10.1098/rspa.1959.0200
    Used for: the vectorial focus-field model behind PSFGenerator's Richards & Wolf PSF (Renderer.PsfModel = RichardsWolf); the aplanatic system's (cos theta)^(1/2) apodization from energy conservation under the sine condition, i.e. equal power per object-space solid angle (the free imager's collected column, excitation.js collectionRings). Checked: bibliographic details from the Crossref DOI record; named as the source of the Richards & Wolf model on the PSFGenerator page (bigwww.epfl.ch/algorithms/psfgenerator); the apodization is the standard result of its section 2, written from the formula (the paper is not open; not re-read).
  • ries2012 -- Ries J, Kaplan C, Platonova E, Eghlidi H, Ewers H (2012). A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nature Methods 9 582-584. doi:10.1038/nmeth.1991
    Used for: anti-GFP nanobody labelling with minimal linkage error (abstract; no number taken). Checked: PubMed abstract only.
  • rivetti1996 -- Rivetti C, Guthold M, Bustamante C (1996). Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. Journal of Molecular Biology 264 919-932. doi:10.1006/jmbi.1996.0687
    Used for: DNA deposited on a surface can equilibrate on it as a two-dimensional worm-like chain (abstract): the nanorulers' in-plane bending model. Its 2D statistics (tangent correlation exp(-s/2Lp); mean square end-to-end distance = the 3D formula with Lp -> 2Lp) are derived on the nanorulers page, not quoted. Checked: citation and abstract via PubMed (PMID 9000621); full text not open.
  • sage2019 -- Sage D, Pham T-A, Babcock H, Lukes T, Pengo T, Chao J, Velmurugan R, Herbert A, Agrawal A, Colabrese S, Wheeler A, Archetti A, Rieger B, Ober R, Hagen GM, Sibarita J-B, Ries J, Henriques R, Unser M, Holden S (2019). Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software. Nature Methods 16 387-395. doi:10.1038/s41592-019-0364-4 (PMC6684258)
    Used for: the SMLM Challenge (simulated 2D, astigmatic, biplane and double-helix datasets): the comparison of the PSF and noise models in docs/dev/vectorial-psf-step4-smlm-challenge-comparison.md. Checked: citation and abstract via PubMed.
  • scheckenbach2020 -- Scheckenbach M, Bauer J, Zähringer J, Selbach F, Tinnefeld P (2020). DNA origami nanorulers and emerging reference structures. APL Materials 8 110902. doi:10.1063/5.0022885
    Used for: the typical DNA origami nanoruler is a 12-helix bundle about 200 nm long and about 13 nm in diameter (p. 110902-3, Sec. I.A; Fig. 1(e)); three equidistant spots along a 12-helix bundle as a resolution test (Sec. II, Fig. 2(a)); marks placed with an accuracy commonly better than 2 nm (Sec. II): the 80 nm nanoruler's body. Checked: values read from the open-access full text (LMU repository PDF).
  • schlichthaerle2019 -- Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R (2019). Direct visualization of single nuclear pore complex proteins using genetically-encoded probes for DNA-PAINT. Angewandte Chemie International Edition 58 13004-13008. doi:10.1002/anie.201905685 (PMC6771475)
    Used for: DNA-PAINT of Nup96-SNAP/-Halo in U2OS: labelling efficiency about 30 % (main text, Suppl. Table 5); the Nup96 pair 12 nm apart (Fig. 3c); ring separation about 61 nm in 3D DNA-PAINT (Fig. 3d). Checked: Europe PMC full text; the SI (imager dye) not read.
  • schnitzbauer2017 -- Schnitzbauer J, Strauss MT, Schlichthaerle T, Schueder F, Jungmann R (2017). Super-resolution microscopy with DNA-PAINT. Nature Protocols 12 1198-1228. doi:10.1038/nprot.2017.024
    Used for: DNA-PAINT protocol: imager concentrations (sub-nM to nM), bright times, unbound-imager background. Checked: citation via Europe PMC.
  • schueder2019 -- Schueder F, Stein J, Stehr F, Auer A, Sperl B, Strauss MT, Schwille P, Jungmann R (2019). An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions. Nature Methods 16 1101-1104. doi:10.1038/s41592-019-0584-7
    Used for: faster association with optimized sequences (context for k_on). Checked: citation via Europe PMC.
  • soeller2025 -- Soeller C, Bokhobza AFE, Casares-Arias J, Clowsley AH (2025). Optimizing effective labeling efficiency in MINFLUX 3D DNA-PAINT microscopy by maximizing marker detection probability. ACS Photonics 13 14-27. doi:10.1021/acsphotonics.5c01253 (PMC12784405)
    Used for: DNA-PAINT effective labelling efficiency of U-2 OS Nup96-mEGFP with anti-GFP nanobody docking strands: 54.6-68.2 % (Results). Checked: Europe PMC full text.
  • steelman2017 -- Steelman ZA, Eldridge WJ, Weintraub JB, Wax A (2017). Is the nuclear refractive index lower than cytoplasm? Validation of phase measurements and implications for light scattering technologies. Journal of Biophotonics 10 1714-1722. doi:10.1002/jbio.201600314 (PMC5647217)
    Used for: refractive indices at 540 nm from quantitative phase images of freshly plated (spherical) cells and isolated nuclei of four cell lines (MCF-7, A549, BEAS-2B, HVE): whole cells 1.3568-1.3775, nuclei 1.3427-1.3527, the nucleus below the cytoplasm; PBS 1.335 (Methods 2.3, Results 3.1): the scale of the BrightField index defaults. Checked: values read from the Europe PMC full text (PMC5647217).
  • subach2009 -- Subach FV, Patterson GH, Manley S, Gillette JM, Lippincott-Schwartz J, Verkhusha VV (2009). Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nature Methods 6 153-159. doi:10.1038/nmeth.1298
    Used for: PAmCherry1/2 (the PAmCherry2 entry borrows PAmCherry1's On-state spectra: FPbase has none for PAmCherry2). Checked: citation via Europe PMC.
  • theiss2023 -- Theiss M, Hériché JK, Russell C, Helekal D, Soppitt A, Ries J, Ellenberg J, Brazma A, Uhlmann V (2023). Simulating structurally variable nuclear pore complexes for microscopy. Bioinformatics 39 btad587. doi:10.1093/bioinformatics/btad587 (PMC10570993)
    Used for: CIR4MICS, the NPC simulator webSMLM cites for its parametrised Nup96 geometry (its variability models are not implemented here). Checked: PubMed metadata and abstract (PMID 37756700); the OUP article page.
  • thermofisher_fluospheres -- Thermo Fisher Scientific (2026). Summary of Molecular Probes FluoSpheres fluorescent microspheres (The Molecular Probes Handbook, table). https://www.thermofisher.com/home/references/molecular-probes-the-handbook/tables/summary-of-molecular-probes-fluospheres-fluorescent-microspheres.html
    Used for: nominal excitation/emission maxima of FluoSpheres yellow-green (505/515), orange (540/560) and red (580/605); the dark red (660/680), infrared (715/755) and TetraSpeck (360/430, 505/515, 560/580, 660/680) maxima are as balinovic2019 quotes them. Checked: vendor table, read online 2026-10-22.
  • thevathasan2019 -- Thevathasan JV, Kahnwald M, Cieśliński K, Hoess P, Peneti SK, Reitberger M, Heid D, Kasuba KC, Hoerner SJ, Li Y, Wu YL, Mund M, Matti U, Pereira PM, Henriques R, Nijmeijer B, Kueblbeck M, Sabinina VJ, Ellenberg J, Ries J (2019). Nuclear pores as versatile reference standards for quantitative superresolution microscopy. Nature Methods 16 1045-1053. doi:10.1038/s41592-019-0574-9 (PMC6768092)
    Used for: Nup96 geometry: 32 copies per NPC in a cytoplasmic and a nucleoplasmic ring, 8 corners per ring with two Nup96 12 nm apart (Results, Fig. 1a-e); radius 53.7 +/- 2.1 nm with SNAP labels (Fig. 2a-c), 64.3 nm antibody-labelled; ring separation 49.3 +/- 5.2 nm (Fig. 2d-f); azimuthal shift between the rings 8.8 deg (Fig. 2g,h; not modelled). Effective labelling efficiencies (Fig. 3i): SNAP + BG-AF647 58 %, mMaple 58 %, anti-GFP nanobodies 62-74 %, indirect immunofluorescence 65 %, HaloTag 21-40 %. Labels: Nup96-SNAP (dSTORM), Nup96-mMaple (PALM), Nup96-mEGFP; no DNA-PAINT. The lower nuclear envelope of U2OS is flat and close to the coverslip (Fig. 1a). Checked: Europe PMC full text (Results) and the PMC figure callouts; a Publisher Correction (Nat Methods 16:1332) not read.
  • thibos2002 -- Thibos LN, Applegate RA, Schwiegerling JT, Webb R; VSIA Standards Taskforce Members (2002). Standards for reporting the optical aberrations of eyes. Journal of Refractive Surgery 18 S652-S660. doi:10.3928/1081-597X-20020901-30
    Used for: the OSA/ANSI Zernike polynomials and their single index j = (n(n+2)+m)/2 (Renderer.PsfZernikeCoefficients, Simulation/SMLMZernike.h). Checked: citation and abstract via PubMed; the full text was not available, so the single-index formula is the one used in the code, not re-read from the paper.
  • tilney1973 -- Tilney LG, Bryan J, Bush DJ, Fujiwara K, Mooseker MS, Murphy DB, Snyder DH (1973). Microtubules: evidence for 13 protofilaments. Journal of Cell Biology 59 267-275. doi:10.1083/jcb.59.2.267 (PMC2109099)
    Used for: 13 equally spaced protofilaments in cellular microtubules (seven kinds, the mitotic apparatus among them). Checked: citation and abstract via PubMed.
  • tokunaga2008 -- Tokunaga M, Imamoto N, Sakata-Sogawa K (2008). Highly inclined thin illumination enables clear single-molecule imaging in cells. Nature Methods 5 159-161. doi:10.1038/nmeth1171
    Used for: HILO: a highly inclined, thin beam (refracted at the coverslip) lights a sheet through the sample; about eightfold the signal-to-background of epi illumination (abstract). The sheet geometry here (thickness = beam FWHM / (tan theta_s cos theta_i) on the axis) is derived, not taken from the paper. Checked: citation and abstract via PubMed (not open access).
  • turkowyd2017 -- Turkowyd B, Balinovic A, Virant D, Carnero HGG, Caldana F, Endesfelder M, Bourgeois D, Endesfelder U (2017). A General Mechanism of Photoconversion of Green-to-Red Fluorescent Proteins Based on Blue and Infrared Light Reduces Phototoxicity in Live-Cell Single-Molecule Imaging. Angewandte Chemie International Edition 56 11634-11639. doi:10.1002/anie.201702870
    Used for: primed conversion (blue priming + near-infrared conversion) of green-to-red FPs; Dendra2-type proteins convert well, wild-type mEos-type poorly (residue 69). Checked: citation and abstract via Europe PMC; no rate constants taken from it (the primed coefficients are estimates).
  • weber1978 -- Weber K, Rathke PC, Osborn M (1978). Cytoplasmic microtubular images in glutaraldehyde-fixed tissue culture cells by electron microscopy and by immunofluorescence microscopy. Proceedings of the National Academy of Sciences of the USA 75 1820-1824. doi:10.1073/pnas.75.4.1820 (PMC392432)
    Used for: cytoplasmic microtubules about 250 A (25 nm) in diameter, about 600 A (60 nm) when decorated by primary and secondary antibodies (abstract): the scale of an antibody label's displacement. Checked: citation and abstract via PubMed.
  • yang1996 -- Yang F, Moss LG, Phillips GN Jr (1996). The molecular structure of green fluorescent protein. Nature Biotechnology 14 1246-1251. doi:10.1038/nbt1096-1246
    Used for: GFP is a cylinder of 11 beta strands with an alpha helix inside; the fluorophores are protected inside the cylinders (abstract). Checked: PubMed abstract (PMID 9631087).
  • zhang2007 -- Zhang B, Zerubia J, Olivo-Marin J-C (2007). Gaussian approximations of fluorescence microscope point-spread function models. Applied Optics 46 1819-1829. doi:10.1364/AO.46.001819
    Used for: the Gaussian approximation of the in-focus widefield PSF, sigma = 0.21 lambda/NA (Renderer.PsfModel = Gaussian). Checked: citation and abstract via PubMed; the full text was not open: sigma = 0.21 lambda/NA as quoted from it by Linden et al. 2017 (Nat Commun 8:15115, PMC5418599, Methods 'Prior distributions').
  • zhang2012 -- Zhang M, Chang H, Zhang Y, Yu J, Wu L, Ji W, Chen J, Liu B, Lu J, Liu Y, Zhang J, Xu P, Xu T (2012). Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nature Methods 9 727-729. doi:10.1038/nmeth.2021
    Used for: mEos3.2. Checked: citation and abstract via Europe PMC.
  • zuo2017 -- Zuo C, Sun J, Li J, Zhang J, Asundi A, Chen Q (2017). High-resolution transport-of-intensity quantitative phase microscopy with annular illumination. Scientific Reports 7 7654. doi:10.1038/s41598-017-06837-1 (PMC5550517)
    Used for: Koehler illumination as the incoherent sum of the coherent images of all condenser source points (Abbe's method; Eqs. 1-2), defocus as an angular-spectrum factor in the objective pupil, and the weak-object phase transfer function odd in defocus (no phase contrast in focus, opposite signs at +/- dz): the BrightField model and its contrast through focus. Checked: read from the Europe PMC full text (PMC5550517).