@article{BerberichKurzReinhardetal.2021,
  author    = {Berberich, Andreas and Kurz, Andreas and Reinhard, Sebastian and Paul, Torsten Johann and Burd, Paul Ray and Sauer, Markus and Kollmannsberger, Philip},
  title     = {Fourier Ring Correlation and anisotropic kernel density estimation improve deep learning based SMLM reconstruction of microtubules},
  series = {Frontiers in Bioinformatics},
  volume    = {1},
  journal   = {Frontiers in Bioinformatics},
  doi       = {10.3389/fbinf.2021.752788},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-261686},
  year      = {2021},
  abstract  = {Single-molecule super-resolution microscopy (SMLM) techniques like dSTORM can reveal biological structures down to the nanometer scale. The achievable resolution is not only defined by the localization precision of individual fluorescent molecules, but also by their density, which becomes a limiting factor e.g., in expansion microscopy. Artificial deep neural networks can learn to reconstruct dense super-resolved structures such as microtubules from a sparse, noisy set of data points. This approach requires a robust method to assess the quality of a predicted density image and to quantitatively compare it to a ground truth image. Such a quality measure needs to be differentiable to be applied as loss function in deep learning. We developed a new trainable quality measure based on Fourier Ring Correlation (FRC) and used it to train deep neural networks to map a small number of sampling points to an underlying density. Smooth ground truth images of microtubules were generated from localization coordinates using an anisotropic Gaussian kernel density estimator. We show that the FRC criterion ideally complements the existing state-of-the-art multiscale structural similarity index, since both are interpretable and there is no trade-off between them during optimization. The TensorFlow implementation of our FRC metric can easily be integrated into existing deep learning workflows.},
  language  = {en}
}
@phdthesis{Burd2022,
  author    = {Burd, Paul Ray},
  title     = {Multiwavelength Probes of Physical Conditions in the Blazar Zone of AGN jets},
  doi       = {10.25972/OPUS-29700},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-297001},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Context. In active galaxies, matter is accreted onto super massive black holes (SMBH). This accretion process causes a region roughly the size of our solar system to outshine the entire host galaxy, forming an active galactic nucleus (AGN). In some of these active galaxies, highly relativistic particle jets are formed parallel to the rotation axis of the super massive black hole. A fraction of these sources is observed under a small inclination angle between the pointing direction of the jet and the observing line of sight. These sources are called blazars. Due to the small inclination angle and the highly relativistic speeds of the particles in the jet, beaming effects occur in the radiation of these particles. Blazars can be subdivided into the high luminosity flat spectrum radio quasars (FSRQs) and the low luminosity BL Lacertae objects (BL Lacs). As all AGN, blazars are broadband emitters and therefore observable from the longest wavelengths in the radio regime to the shortest wavelengths in the gamma-ray regime. In this thesis I will analyze blazars at these two extremes with respect to their parsec-scale properties in the radio and their time evolution properties in gamma-ray flux. Method. In the radio regime the technique of very long baseline interferometry (VLBI) can be used in order to spatially resolve the synchrotron radiation coming from those objects down to sub-parsec scales. This information can be used to observe the time evolution of the structure of such sources. This is done in large monitoring programs such as the MOJAVE (15 GHz) and the Boston University blazar monitoring program (43 GHz). In this thesis I utilize data of 28 sources from these monitoring programs spanning 10 years of observation from 2003 to 2013, resulting in over 1800 observed epochs, to study the brightness temperature and diameter gradients of these jets. I conduct a search for systematic geometry transitions in the radio jets. The synchrotron cooling time in the radio core of the jets is used to determine the magnetic field strength in the radio core. Considering the jet geometry, these magnetic field strengths are scaled to the ergosphere of the SMBH in order to obtain the distance of the radio core to the SMBH. In the gamma-regime these blazars cannot be spatially resolved. Due to this, it is hard to put strong constrains onto where the gamma-ray emitting region is. Blazars have shown to be variable at high energies on time scales down to minutes. The nature of this variability can be studied in order to put constrains on the particle acceleration mechanism and possibly the region and size of the gamma-ray emitting region. The variability of blazars in the energy range between 0.1 GeV and 1 GeV can for example be observed with the pair-conversion telescope on board the Fermi satellite. I use 10 years of data from the Fermi-LAT (LAT: Large Area Telescope) satellite in order to study the variability of a large sample of blazars (300-800, depending on the used significance filters for data points). I quantify this variability with the Ornstein-Uhlenbeck (OU) parameters and the power spectral density (PSD) slopes. The same procedure is applied to 20 light curves available for the radio sample. Results. The diameter evolution along the jet axis of the radio sources suggests, that FSRQs feature flatter gradients than BL Lacs. Fitting these gradients, it is revealed that BL Lacs are systematically better described by a simple single power law than FSRQs. I found 9 sources with a strongly constrained geometry transition. The sources are 0219+421, 0336-019, 0415+379, 0528+134, 0836+710, 1101+384, 1156+295, 1253-055 and 2200+420. In all of these sources, the geometry transition regions are further out in the jet than the Bondi sphere. The magnetic field strengths of BL Lacs is systematically larger than that of FSRQs. However the scaling of these fields suggest that the radio cores of BL Lac objects are closer to the SMBHs than the radio cores of FSRQs. Analyzing the variability of Fermi-LAT light curves yields consistent results for all samples. FSRQs show systematically steeper PSD slopes and feature OU parameters more favorable to strong variability than BL Lacs. The Fermi-LAT light curves of the sub-sample of radio jets, suggest an anticorrelation between the jet complexity from the radio observations and the OU-parameters as well as the PSD slopes from the gamma-ray observations. Conclusion. The flatter diameter gradients of FSRQs suggest that these sources are more collimated further down the jet than BL Lacs. The systematically better description of the diameter and brightness temperature gradient by a single power law of BL Lacs, suggest that FSRQs are more complex with respect to the diameter evolution along the jet and the surface brightness distribution than BL Lac objects. FSRQs often feature regions where recollimation can occur in distinct knots within the jets. For the sources where a geometry transition could be constrained, the Bondi radius, being systematically smaller than the position of the transition region along the jet axis, suggest that changing pressure gradients are not the sole cause for these systematic geometry transitions. Nevertheless they may be responsible for recollimation regions, found typically downstream the jet, beyond the Bondi radius and the transition zone. The difference in the distance of the radio cores between FSRQs and BL Lacs is most likely due to the combination of differences in SMBH masses and systematically smaller jet powers in BL Lacs. The variability in energy ranges above 100 MeV and above 1 GeV-regime suggest that many light curves of BL Lac objects are more likely to be white noise while the PSD slopes and the OU parameters of FSRQ gamma-ray light curves favor stronger variability on larger time scales with respect to the time binning of the analyzed light curve. Although the anticorrelation of the jet complexity acquired from the radio observations and the PSD slopes and OU parameters from the gamma-observations suggest that more complex sources favor OU parameters and PSD slopes resulting in more variability (not white noise) it is beyond the scope of this thesis to pinpoint whether this correlation results from causation. The question whether a complex jet causes more gamma-ray variability or more gamma-ray variability causes more complex jets cannot be answered at this point. Nevertheless the computed correlation measures suggest that this dependence is most likely not linear and therefore an indication that these effects might even interact.},
  language  = {en}
}