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The joint probability distribution of matter overdensity and galaxy counts in cells is a powerful probe of cosmology, and the extent to which variance in galaxy counts at fixed matter density deviates from Poisson shot noise is not fully understood. The lack of informed bounds on this stochasticity is currently the limiting factor in constraining cosmology with the galaxy-matter PDF. We investigate stochasticity in the conditional distribution of galaxy counts at fixed matter density and present a halo occupation distribution (HOD)-based approach for obtaining plausible ranges for stochasticity parameters. To probe the high-dimensional space of possible galaxy-matter connections, we derive HODs which conserve linear galaxy bias and number density to produce redMaGiC-like galaxy catalogs within the AbacusSummit suite of N-body simulations. We study the impact of individual HOD parameters and cosmology on stochasticity and perform a Monte Carlo search in HOD parameter space, subject to the constraints on bias and density. In mock catalogs generated by the selected HODs, shot noise in galaxy counts spans both sub-Poisson and super-Poisson values, ranging from 80% to 133% of Poisson variance at mean matter density. Nearly all derived HODs show a positive relationship between local matter density and stochasticity. For galaxy catalogs with higher stochasticity, quadratic galaxy bias is required for an accurate description of the conditional PDF of galaxy counts at fixed matter density. The presence of galaxy assembly bias also substantially extends the range of stochasticity in the super-Poisson direction. This HOD-based approach leverages degrees of freedom in the galaxy-halo connection to obtain informed bounds on model nuisance parameters and can be adapted to other parametrizations of stochasticity, in particular to motivate prior ranges for cosmological analyses., Comment: Submitted to Astronomy and Astrophysics

The holographic principle suggests that regions of space contain fewer physical degrees of freedom than would be implied by conventional quantum field theory. Meanwhile, in Hilbert spaces of large dimension $2^n$, it is possible to define $N \gg n$ Pauli algebras that are nearly anti-commuting (but not quite) and which can be thought of as "overlapping degrees of freedom". We propose to model the phenomenology of holographic theories by allowing field-theory modes to be overlapping, and derive potential observational consequences. In particular, we build a Fermionic quantum field whose effective degrees of freedom approximately obey area scaling and satisfy a cosmic Bekenstein bound, and compare predictions of that model to cosmic neutrino observations. Our implementation of holography implies a finite lifetime of plane waves, which depends on the overall UV cutoff of the theory. To allow for neutrino flux from blazar TXS 0506+056 to be observable, our model needs to have a cutoff $k_{\mathrm{UV}} \lesssim 500\, k_{\mathrm{LHC}}\,$. This is broadly consistent with current bounds on the energy spectrum of cosmic neutrinos from IceCube, but high energy neutrinos are a potential challenge for our model of holography. We motivate our construction via quantum mereology, i.e. using the idea that EFT degrees of freedom should emerge from an abstract theory of quantum gravity by finding quasi-classical Hilbert space decompositions. We also discuss how to extend the framework to Bosons. Finally, using results from random matrix theory we derive an analytical understanding of the energy spectrum of our theory. The numerical tools used in this work are publicly available within the GPUniverse package, https://github.com/OliverFHD/GPUniverse ., Comment: 46 pages + appendix; code and data available at https://github.com/OliverFHD/GPUniverse

We present the integrated 3-point correlation functions (3PCF) involving both the cosmic shear and the galaxy density fields. These are a set of higher-order statistics that describe the modulation of local 2-point correlation functions (2PCF) by large-scale features in the fields, and which are easy to measure from galaxy imaging surveys. Based on previous works on the shear-only integrated 3PCF, we develop the theoretical framework for modelling 5 new statistics involving the galaxy field and its cross-correlations with cosmic shear. Using realistic galaxy and cosmic shear mocks from simulations, we determine the regime of validity of our models based on leading-order standard perturbation theory with an MCMC analysis that recovers unbiased constraints of the amplitude of fluctuations parameter $A_s$ and the linear and quadratic galaxy bias parameters $b_1$ and $b_2$. Using Fisher matrix forecasts for a DES-Y3-like survey, relative to baseline analyses with conventional 3$\times$2PCFs, we find that the addition of the shear-only integrated 3PCF can improve cosmological parameter constraints by $20-40\%$. The subsequent addition of the new statistics introduced in this paper can lead to further improvements of $10-20\%$, even when utilizing only conservatively large scales where the tree-level models are valid. Our results motivate future work on the galaxy and shear integrated 3PCFs, which offer a practical way to extend standard analyses based on 3$\times$2PCFs to systematically probe the non-Gaussian information content of cosmic density fields., Comment: 19 pages, 8 figures + appendix. Comments are welcome!

We report Tensorial tomographic Fourier Ptychography (ToFu), a new non-scanning label-free tomographic microscopy method for simultaneous imaging of quantitative phase and anisotropic specimen information in 3D. Built upon Fourier Ptychography, a quantitative phase imaging technique, ToFu additionally highlights the vectorial nature of light. The imaging setup consists of a standard microscope equipped with an LED matrix, a polarization generator, and a polarization-sensitive camera. Permittivity tensors of anisotropic samples are computationally recovered from polarized intensity measurements across three dimensions. We demonstrate ToFu's efficiency through volumetric reconstructions of refractive index, birefringence, and orientation for various validation samples, as well as tissue samples from muscle fibers and diseased heart tissue. Our reconstructions of muscle fibers resolve their 3D fine-filament structure and yield consistent morphological measurements compared to gold-standard second harmonic generation scanning confocal microscope images found in the literature. Additionally, we demonstrate reconstructions of a heart tissue sample that carries important polarization information for detecting cardiac amyloidosis.

We study gravitational back-reaction within relational time formulations of quantum mechanics by considering two versions of time: a time coordinate, modelled as a global quantum degree of freedom, and the proper time of a given physical system, modelled via an internal degree of freedom serving as a local quantum "clock". We show that interactions between coordinate time and mass-energy in a global Wheeler-DeWitt-like constraint lead to gravitational time dilation. In the presence of a massive object this agrees with time dilation in a Schwarzchild metric at leading order in $G$. Furthermore, if two particles couple independently to the time coordinate we show that Newtonian gravitational interaction between those particles emerges in the low energy limit. We also observe features of renormalization of high energy divergences., Comment: Essay written for the Gravity Research Foundation's 2023 Awards for Essays on Gravitation

The integrated shear 3-point correlation function $\zeta_{\pm}$ measures the correlation between the local shear 2-point function $\xi_{\pm}$ and the 1-point shear aperture mass in patches of the sky. Unlike other higher-order statistics, $\zeta_{\pm}$ can be efficiently measured from cosmic shear data, and it admits accurate theory predictions on a wide range of scales as a function of cosmological and baryonic feedback parameters. Here, we develop and test a likelihood analysis pipeline for cosmological constraints using $\zeta_{\pm}$. We incorporate treatment of systematic effects from photometric redshift uncertainties, shear calibration bias and galaxy intrinsic alignments. We also develop an accurate neural-network emulator for fast theory predictions in MCMC parameter inference analyses. We test our pipeline using realistic cosmic shear maps based on $N$-body simulations with a DES Y3-like footprint, mask and source tomographic bins, finding unbiased parameter constraints. Relative to $\xi_{\pm}$-only, adding $\zeta_{\pm}$ can lead to $\approx 10-25\%$ improvements on the constraints of parameters like $A_s$ (or $\sigma_8$) and $w_0$. We find no evidence in $\xi_{\pm} + \zeta_{\pm}$ constraints of a significant mitigation of the impact of systematics. We also investigate the impact of the size of the apertures where $\zeta_{\pm}$ is measured, and of the strategy to estimate the covariance matrix ($N$-body vs. lognormal). Our analysis solidifies the strong potential of the $\zeta_{\pm}$ statistic and puts forward a pipeline that can be readily used to improve cosmological constraints using real cosmic shear data., Comment: 21 pages, 11 figures, 3 tables. Comments welcome

Until recently, conventional biochemical staining had the undisputed status as well-established benchmark for most biomedical problems related to clinical diagnostics, fundamental research and biotechnology. Despite this role as gold-standard, staining protocols face several challenges, such as a need for extensive, manual processing of samples, substantial time delays, altered tissue homeostasis, limited choice of contrast agents for a given sample, 2D imaging instead of 3D tomography and many more. Label-free optical technologies, on the other hand, do not rely on exogenous and artificial markers, by exploiting intrinsic optical contrast mechanisms, where the specificity is typically less obvious to the human observer. Over the past few years, digital staining has emerged as a promising concept to use modern deep learning for the translation from optical contrast to established biochemical contrast of actual stainings. In this review article, we provide an in-depth analysis of the current state-of-the-art in this field, suggest methods of good practice, identify pitfalls and challenges and postulate promising advances towards potential future implementations and applications., Comment: Review article, 4 main Figures, 3 Tables, 2 supplementary figures

Key non-Gaussian properties of cosmological fields can be captured by their one-point statistics, providing a complement to two-point statistical measurements from power spectra or correlation functions. Large deviation theory can robustly predict the one-point statistics of cosmological density fields on mildly non-linear scales from first principles. It provides a direct prediction for the cumulant generating function (CGF) of such fields, from which a prediction for the more commonly used probability density function (PDF) is extracted through an inverse Laplace transform. For joint one-point statistics of multiple fields, the inverse Laplace transform rapidly becomes more cumbersome and computationally expensive. In this work, we demonstrate for the first time that the weak lensing CGF itself can be used as an observable that captures an equal amount of cosmological information to the PDF. While we use the weak-lensing convergence field as a simplistic and instructive example, this work is intended as a first step towards a cosmological analysis based on large deviation theory in the context of a nulling framework, which excludes contributions from small scales to facilitate highly accurate theoretical predictions. In this context, the method should be generally applicable for a multi-scale tomographic analysis of weak lensing and galaxy clustering., Comment: Accepted by the Open Journal of Astrophysics

Deep learning (DL) shows notable success in biomedical studies. However, most DL algorithms work as a black box, exclude biomedical experts, and need extensive data. We introduce the Self-Enhancing Multi-Photon Artificial Intelligence (SEMPAI), that integrates hypothesis-driven priors in a data-driven DL approach for research on multiphoton microscopy (MPM) of muscle fibers. SEMPAI utilizes meta-learning to optimize prior integration, data representation, and neural network architecture simultaneously. This allows hypothesis testing and provides interpretable feedback about the origin of biological information in MPM images. SEMPAI performs joint learning of several tasks to enable prediction for small datasets. The method is applied on an extensive multi-study dataset resulting in the largest joint analysis of pathologies and function for single muscle fibers. SEMPAI outperforms state-of-the-art biomarkers in six of seven predictive tasks, including those with scarce data. SEMPAI's DL models with integrated priors are superior to those without priors and to prior-only machine learning approaches.

One-point probability distribution functions (PDFs) of the cosmic matter density are powerful cosmological probes that extract non-Gaussian properties of the matter distribution and complement two-point statistics. Computing the covariance of one-point PDFs is key for building a robust galaxy survey analysis for upcoming surveys like Euclid and the Rubin Observatory LSST and requires good models for the two-point PDFs characterising spatial correlations. In this work, we obtain accurate PDF covariances using effective shifted lognormal two-point PDF models for the mildly non-Gaussian weak lensing convergence and validate our predictions against large sets of Gaussian and non-Gaussian maps. We show how the dominant effects in the covariance matrix capturing super-sample covariance arise from a large-separation expansion of the two-point PDF and discuss differences between the covariances obtained from small patches and full sky maps. Finally, we describe how our formalism can be extended to characterise the PDF covariance for 3D-dimensional spectroscopic fields using the 3D matter PDF as an example. We describe how covariances from simulated boxes with fixed overall density can be supplemented with the missing super-sample covariance effect by relying on theoretical predictions validated against separate-universe style simulations., Comment: 29 pages, 24 figures

Context. Weak lensing and clustering statistics beyond two-point functions can capture non-Gaussian information about the matter density field, thereby improving the constraints on cosmological parameters relative to the mainstream methods based on correlation functions and power spectra. Aims. This paper presents a cosmological analysis of the fourth data release of the Kilo Degree Survey based on the density split statistics, which measures the mean shear profiles around regions classified according to foreground densities. The latter is constructed from a bright galaxy sample, which we further split into red and blue samples, allowing us to probe their respective connection to the underlying dark matter density. Methods. We use the state-of-the-art model of the density splitting statistics and validate its robustness against mock data infused with known systematic effects such as intrinsic galaxy alignment and baryonic feedback. Results. After marginalising over the photometric redshift uncertainty and the residual shear calibration bias, we measure for the full KiDS-bright sample a structure growth parameter of $S_8 = \sigma_8 \sqrt{\Omega_\mathrm{m}/0.3} = 0.74^{+0.03}_{-0.02}$ that is competitive to and consistent with two-point cosmic shear results, a matter density of $\Omega_\mathrm{m} = 0.28 \pm 0.02$, and a constant galaxy bias of $b = 1.32^{+0.12}_{-0.10}$., Comment: 18 pages, 23 Figures

The holographic principle suggests that the Hilbert space of quantum gravity is locally finite-dimensional. Motivated by this point-of-view, and its application to the observable Universe, we introduce a set of numerical and conceptual tools to describe scalar fields with finite-dimensional Hilbert spaces, and to study their behaviour in expanding cosmological backgrounds. These tools include accurate approximations to compute the vacuum energy of a field mode $\mathbf{k}$ as a function of the dimension $d_{\mathbf{k}}$ of the mode Hilbert space, as well as a parametric model for how that dimension varies with $|\mathbf{k}|$. We show that the maximum entropy of our construction momentarily scales like the boundary area of the observable Universe for some values of the parameters of that model. And we find that the maximum entropy generally follows a sub-volume scaling as long as $d_{\mathbf{k}}$ decreases with $|\mathbf{k}|$. We also demonstrate that the vacuum energy density of the finite-dimensional field is dynamical and decays between two constant epochs in our fiducial construction. These results rely on a number of non-trivial modelling choices, but our general framework may serve as a starting point for future investigations of the impact of finite-dimensionality of Hilbert space on cosmological physics., Comment: 22 pages + appendix; public code available at github.com/OliverFHD/GPUniverse

Observational astrophysics consists of making inferences about the Universe by comparing data and models. The credible intervals placed on model parameters are often as important as the maximum a posteriori probability values, as the intervals indicate concordance or discordance between models and with measurements from other data. Intermediate statistics (e.g. the power spectrum) are usually measured and inferences made by fitting models to these rather than the raw data, assuming that the likelihood for these statistics has multivariate Gaussian form. The covariance matrix used to calculate the likelihood is often estimated from simulations, such that it is itself a random variable. This is a standard problem in Bayesian statistics, which requires a prior to be placed on the true model parameters and covariance matrix, influencing the joint posterior distribution. As an alternative to the commonly-used Independence-Jeffreys prior, we introduce a prior that leads to a posterior that has approximately frequentist matching coverage. This is achieved by matching the covariance of the posterior to that of the distribution of true values of the parameters around the maximum likelihood values in repeated trials, under certain assumptions. Using this prior, credible intervals derived from a Bayesian analysis can be interpreted approximately as confidence intervals, containing the truth a certain proportion of the time for repeated trials. Linking frequentist and Bayesian approaches that have previously appeared in the astronomical literature, this offers a consistent and conservative approach for credible intervals quoted on model parameters for problems where the covariance matrix is itself an estimate., Comment: 15 pages, 6 figures, version accepted by MNRAS

We study the connection of matter density and its tracers from the PDF perspective. One aspect of this connection is the conditional expectation value $\langle \delta_{\mathrm{tracer}}|\delta_m\rangle$ when averaging both tracer and matter density over some scale. We present a new way to incorporate a Lagrangian bias expansion of this expectation value into standard frameworks for modelling the PDF of density fluctuations and counts-in-cells statistics. Using N-body simulations and mock galaxy catalogs we confirm the accuracy of this expansion and compare it to the more commonly used Eulerian parametrization. For halos hosting typical luminous red galaxies, the Lagrangian model provides a significantly better description of $\langle \delta_{\mathrm{tracer}}|\delta_m\rangle$ at second order in perturbations. A second aspect of the matter-tracer connection is shot-noise, \ie the scatter of tracer density around $\langle \delta_{\mathrm{tracer}}|\delta_m\rangle$. It is well known that this noise can be significantly non-Poissonian and we validate the performance of a more general, two-parameter shot-noise model for different tracers and simulations. Both parts of our analysis are meant to pave the way for forthcoming applications to survey data., Comment: 20 pages, submitted to MNRAS, numerical tools available at https://github.com/OliverFHD/CosMomentum

Studying the statistical properties of the large-scale structure in the Universe with weak gravitational lensing is a prime goal of several current and forthcoming galaxy surveys. The power that weak lensing has to constrain cosmological parameters can be enhanced by considering statistics beyond second-order shear correlation functions or power spectra. One such higher-order probe that has proven successful in observational data is the density split statistics (DSS), in which one analyses the mean shear profiles around points that are classified according to their foreground galaxy density. In this paper, we generalise the most accurate DSS model to allow for a broad class of angular filter functions used for the classification of the different local density regions. This approach is motivated by earlier findings showing that an optimised filter can provide tighter constraints on model parameters compared to the standard top-hat case. We build on large deviation theory approaches and approximations thereof to model the matter density PDF, and on perturbative calculations of higher-order moments of the density field. The novel addition relies on the generalisation of these previously employed calculations to allow for general filter functions and is validated on several sets of numerical simulations. The revised model fits well the simulation measurements, with a residual systematic offset that is small compared to the statistical accuracy of current weak lensing surveys. The accuracy of the model is slightly lower for a compensated filter than for a non-negative filter function, and that it increases with the filter size. Using a Fisher matrix approach, we find constraints comparable to the commonly used two-point cosmic shear measures. Hence, our DSS model can be used in competitive analyses of current cosmic shear data, while it may need refinements for forthcoming lensing surveys., Comment: 21 pages, 13 figures

We present the integrated 3-point shear correlation function $i\zeta_{\pm}$ -- a higher-order statistic of the cosmic shear field -- which can be directly estimated in wide-area weak lensing surveys without measuring the full 3-point shear correlation function, making this a practical and complementary tool to 2-point statistics for weak lensing cosmology. We define it as the 1-point aperture mass statistic $M_{\mathrm{ap}}$ measured at different locations on the shear field correlated with the corresponding local 2-point shear correlation function $\xi_{\pm}$. Building upon existing work on the integrated bispectrum of the weak lensing convergence field, we present a theoretical framework for computing the integrated 3-point function in real space for any projected field within the flat-sky approximation and apply it to cosmic shear. Using analytical formulae for the non-linear matter power spectrum and bispectrum, we model $i\zeta_{\pm}$ and validate it on N-body simulations within the uncertainties expected from the sixth year cosmic shear data of the Dark Energy Survey. We also explore the Fisher information content of $i\zeta_{\pm}$ and perform a joint analysis with $\xi_{\pm}$ for two tomographic source redshift bins with realistic shape-noise to analyse its power in constraining cosmological parameters. We find that the joint analysis of $\xi_{\pm}$ and $i\zeta_{\pm}$ has the potential to considerably improve parameter constraints from $\xi_{\pm}$ alone, and can be particularly useful in improving the figure of merit of the dynamical dark energy equation of state parameters from cosmic shear data., Comment: Accepted for publication in MNRAS; v2 matches the accepted manuscript; 18 pages + appendix

Pinning down the total neutrino mass and the dark energy equation of state is a key aim for upcoming galaxy surveys. Weak lensing is a unique probe of the total matter distribution whose non-Gaussian statistics can be quantified by the one-point probability distribution function (PDF) of the lensing convergence. We calculate the convergence PDF on mildly non-linear scales from first principles using large-deviation statistics, accounting for dark energy and the total neutrino mass. For the first time, we comprehensively validate the cosmology-dependence of the convergence PDF model against large suites of simulated lensing maps, demonstrating its percent-level precision and accuracy. We show that fast simulation codes can provide highly accurate covariance matrices, which can be combined with the theoretical PDF model to perform forecasts and eliminate the need for relying on expensive N-body simulations. Our theoretical model allows us to perform the first forecast for the convergence PDF that varies the full set of $\Lambda$CDM parameters. Our Fisher forecasts establish that the constraining power of the convergence PDF compares favourably to the two-point correlation function for a Euclid-like survey area at a single source redshift. When combined with a CMB prior from Planck, the PDF constrains both the neutrino mass $M_\nu$ and the dark energy equation of state $w_0$ more strongly than the two-point correlation function., Comment: Accepted by MNRAS