13 research outputs found
Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data
In this study, we introduce Blob-B-Gone, a lightweight framework to computationally differentiate and eventually remove dense isotropic localization accumulations (blobs) caused by artifactually immobilized particles in MINFLUX single-particle tracking (SPT) measurements. This approach uses purely geometrical features extracted from MINFLUX-detected single-particle trajectories, which are treated as point clouds of localizations. Employing k-means++ clustering, we perform single-shot separation of the feature space to rapidly extract blobs from the dataset without the need for training. We automatically annotate the resulting sub-sets and, finally, evaluate our results by means of principal component analysis (PCA), highlighting a clear separation in the feature space. We demonstrate our approach using two- and three-dimensional simulations of freely diffusing particles and blob artifacts based on parameters extracted from hand-labeled MINFLUX tracking data of fixed 23-nm bead samples and two-dimensional diffusing quantum dots on model lipid membranes. Applying Blob-B-Gone, we achieve a clear distinction between blob-like and other trajectories, represented in F1 scores of 0.998 (2D) and 1.0 (3D) as well as 0.995 (balanced) and 0.994 (imbalanced). This framework can be straightforwardly applied to similar situations, where discerning between blob and elongated time traces is desirable. Given a number of localizations sufficient to express geometric features, the method can operate on any generic point clouds presented to it, regardless of its origin
TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data
Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox – 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience
Discovery and Follow-up Observations of the Young Type Ia Supernova 2016coj
The Type~Ia supernova (SN~Ia) 2016coj in NGC 4125 (redshift ) was
discovered by the Lick Observatory Supernova Search 4.9 days after the fitted
first-light time (FFLT; 11.1 days before -band maximum). Our first detection
(pre-discovery) is merely day after the FFLT, making SN 2016coj one
of the earliest known detections of a SN Ia. A spectrum was taken only 3.7 hr
after discovery (5.0 days after the FFLT) and classified as a normal SN Ia. We
performed high-quality photometry, low- and high-resolution spectroscopy, and
spectropolarimetry, finding that SN 2016coj is a spectroscopically normal SN
Ia, but with a high velocity of \ion{Si}{2} 6355 (\,\kms\
around peak brightness). The \ion{Si}{2} 6355 velocity evolution can
be well fit by a broken-power-law function for up to a month after the FFLT. SN
2016coj has a normal peak luminosity ( mag), and it
reaches a -band maximum \about16.0~d after the FFLT. We estimate there to be
low host-galaxy extinction based on the absence of Na~I~D absorption lines in
our low- and high-resolution spectra. The spectropolarimetric data exhibit weak
polarization in the continuum, but the \ion{Si}{2} line polarization is quite
strong () at peak brightness.Comment: Submitte
The Lick AGN Monitoring Project 2016 : dynamical modeling of velocity-resolved Hβ lags in luminous Seyfert galaxies
K.H. acknowledges support from STFC grant ST/R000824/1.We have modeled the velocity-resolved reverberation response of the Hβ broad emission line in nine Seyfert 1 galaxies from the Lick Active Galactic Nucleus (AGN) Monitoring Project 2016 sample, drawing inferences on the geometry and structure of the low-ionization broad-line region (BLR) and the mass of the central supermassive black hole. Overall, we find that the Hβ BLR is generally a thick disk viewed at low to moderate inclination angles. We combine our sample with prior studies and investigate line-profile shape dependence, such as log10(FWHM/σ), on BLR structure and kinematics and search for any BLR luminosity-dependent trends. We find marginal evidence for an anticorrelation between the profile shape of the broad Hβ emission line and the Eddington ratio, when using the rms spectrum. However, we do not find any luminosity-dependent trends, and conclude that AGNs have diverse BLR structure and kinematics, consistent with the hypothesis of transient AGN/BLR conditions rather than systematic trends.Publisher PDFPeer reviewe
The Lick AGN Monitoring Project 2016: Dynamical Modeling of Velocity-Resolved H\b{eta} Lags in Luminous Seyfert Galaxies
We have modeled the velocity-resolved reverberation response of the H\b{eta}
broad emission line in nine Seyfert 1 galaxies from the Lick Active Galactic
Nucleus (AGN) Monitioring Project 2016 sample, drawing inferences on the
geometry and structure of the low-ionization broad-line region (BLR) and the
mass of the central supermassive black hole. Overall, we find that the H\b{eta}
BLR is generally a thick disk viewed at low to moderate inclination angles. We
combine our sample with prior studies and investigate line-profile shape
dependence, such as log10(FWHM/{\sigma}), on BLR structure and kinematics and
search for any BLR luminosity-dependent trends. We find marginal evidence for
an anticorrelation between the profile shape of the broad H\b{eta} emission
line and the Eddington ratio, when using the root-mean-square spectrum.
However, we do not find any luminosity-dependent trends, and conclude that AGNs
have diverse BLR structure and kinematics, consistent with the hypothesis of
transient AGN/BLR conditions rather than systematic trends
The Lick AGN Monitoring Project 2016 : velocity-resolved Hβ lags in luminous Seyfert galaxies
Funding: K.H. acknowledges support from STFC grant ST/R000824/1.We carried out spectroscopic monitoring of 21 low-redshift Seyfert 1 galaxies using the Kast double spectrograph on the 3 m Shane telescope at Lick Observatory from April 2016 to May 2017. Targetingactive galactic nuclei (AGN) with luminosities of λLλ(5100 Å) ≈ 1044 erg s−1 and predicted Hβ lags of∼ 20–30 days or black hole masses of 107–108.5 M⊙, our campaign probes luminosity-dependent trends in broad-line region (BLR) structure and dynamics as well as to improve calibrations for single-epoch estimates of quasar black hole masses. Here we present the first results from the campaign, including Hβ emission-line light curves, integrated Hβ lag times (8–30 days) measured against V -band continuum light curves, velocity-resolved reverberation lags, line widths of the broad Hβ components, and virial black hole mass estimates (107.1–108.1 M⊙). Our results add significantly to the number of existing velocity-resolved lag measurements and reveal a diversity of BLR gas kinematics at moderately high AGN luminosities. AGN continuum luminosity appears not to be correlated with the type of kinematics that its BLR gas may exhibit. Follow-up direct modeling of this dataset will elucidate the detailed kinematics and provide robust dynamical black hole masses for several objects in this sample.Publisher PDFPeer reviewe
The Lick AGN Monitoring Project 2016: Dynamical Modeling of Velocity-resolved Hβ Lags in Luminous Seyfert Galaxies
We have modeled the velocity-resolved reverberation response of the H broad emission line in nine Seyfert 1 galaxies from the Lick Active Galactic Nucleus (AGN) Monitoring Project 2016 sample, drawing inferences on the geometry and structure of the low-ionization broad-line region (BLR) and the mass of the central supermassive black hole. Overall, we find that the H BLR is generally a thick disk viewed at low to moderate inclination angles. We combine our sample with prior studies and investigate line-profile shape dependence, such as , on BLR structure and kinematics and search for any BLR luminosity-dependent trends. We find marginal evidence for an anticorrelation between the profile shape of the broad H emission line and the Eddington ratio, when using the rms spectrum. However, we do not find any luminosity-dependent trends, and conclude that AGNs have diverse BLR structure and kinematics, consistent with the hypothesis of transient AGN/BLR conditions rather than systematic trends
The Lick AGN Monitoring Project 2016:dynamical modeling of velocity-resolved H<i>β</i> lags in luminous Seyfert galaxies
We have modeled the velocity-resolved reverberation response of the Hβ broad emission line in nine Seyfert 1 galaxies from the Lick Active Galactic Nucleus (AGN) Monitoring Project 2016 sample, drawing inferences on the geometry and structure of the low-ionization broad-line region (BLR) and the mass of the central supermassive black hole. Overall, we find that the Hβ BLR is generally a thick disk viewed at low to moderate inclination angles. We combine our sample with prior studies and investigate line-profile shape dependence, such as log10(FWHM/σ), on BLR structure and kinematics and search for any BLR luminosity-dependent trends. We find marginal evidence for an anticorrelation between the profile shape of the broad Hβ emission line and the Eddington ratio, when using the rms spectrum. However, we do not find any luminosity-dependent trends, and conclude that AGNs have diverse BLR structure and kinematics, consistent with the hypothesis of transient AGN/BLR conditions rather than systematic trends
The Lick AGN Monitoring Project 2016: Dynamical Modeling of Velocity-resolved Hβ Lags in Luminous Seyfert Galaxies
We have modeled the velocity-resolved reverberation response of the H broad emission line in nine Seyfert 1 galaxies from the Lick Active Galactic Nucleus (AGN) Monitoring Project 2016 sample, drawing inferences on the geometry and structure of the low-ionization broad-line region (BLR) and the mass of the central supermassive black hole. Overall, we find that the H BLR is generally a thick disk viewed at low to moderate inclination angles. We combine our sample with prior studies and investigate line-profile shape dependence, such as , on BLR structure and kinematics and search for any BLR luminosity-dependent trends. We find marginal evidence for an anticorrelation between the profile shape of the broad H emission line and the Eddington ratio, when using the rms spectrum. However, we do not find any luminosity-dependent trends, and conclude that AGNs have diverse BLR structure and kinematics, consistent with the hypothesis of transient AGN/BLR conditions rather than systematic trends