Robust normalization protocols for multiplexed fluorescence bioimage analysis

study of mapping and interaction of co-localized proteins at a sub-cellular level is important for understanding complex biological phenomena. One of the recent techniques to map co-localized proteins is to use the standard immuno-fluorescence microscopy in a cyclic manner (Nat Biotechnol 24:1270–8, 2006; Proc Natl Acad Sci 110:11982–7, 2013). Unfortunately, these techniques suffer from variability in intensity and positioning of signals from protein markers within a run and across different runs. Therefore, it is necessary to standardize protocols for preprocessing of the multiplexed bioimaging (MBI) data from multiple runs to a comparable scale before any further analysis can be performed on the data. In this paper, we compare various normalization protocols and propose on the basis of the obtained results, a robust normalization technique that produces consistent results on the MBI data collected from different runs using the Toponome Imaging System (TIS). Normalization results produced by the proposed method on a sample TIS data set for colorectal cancer patients were ranked favorably by two pathologists and two biologists. We show that the proposed method produces higher between class Kullback-Leibler (KL) divergence and lower within class KL divergence on a distribution of cell phenotypes from colorectal cancer and histologically normal samples

Exploring CEvNS with NUCLEUS at the Chooz Nuclear Power Plant

Coherent elastic neutrino-nucleus scattering (CE$\nu$NS) offers a unique way to study neutrino properties and to search for new physics beyond the Standard Model. Nuclear reactors are promising sources to explore this process at low energies since they deliver large fluxes of (anti-)neutrinos with typical energies of a few MeV. In this paper, a new-generation experiment to study CE$\nu$NS is described. The NUCLEUS experiment will use cryogenic detectors which feature an unprecedentedly low energy threshold and a time response fast enough to be operated in above-ground conditions. Both sensitivity to low-energy nuclear recoils and a high event rate tolerance are stringent requirements to measure CE$\nu$NS of reactor antineutrinos. A new experimental site, denoted the Very-Near-Site (VNS) at the Chooz nuclear power plant in France is described. The VNS is located between the two 4.25 GW$_{\mathrm{th}}$ reactor cores and matches the requirements of NUCLEUS. First results of on-site measurements of neutron and muon backgrounds, the expected dominant background contributions, are given. In this paper a preliminary experimental setup with dedicated active and passive background reduction techniques is presented. Furthermore, the feasibility to operate the NUCLEUS detectors in coincidence with an active muon-veto at shallow overburden is studied. The paper concludes with a sensitivity study pointing out the promising physics potential of NUCLEUS at the Chooz nuclear power plant

First results from the CRESST-III low-mass dark matter program

The CRESST experiment is a direct dark matter search which aims to measure interactions of potential dark matter particles in an earth-bound detector. With the current stage, CRESST-III, we focus on a low energy threshold for increased sensitivity towards light dark matter particles. In this manuscript we describe the analysis of one detector operated in the first run of CRESST-III (05/2016-02/2018) achieving a nuclear recoil threshold of 30.1eV. This result was obtained with a 23.6g CaWO$_4$ crystal operated as a cryogenic scintillating calorimeter in the CRESST setup at the Laboratori Nazionali del Gran Sasso (LNGS). Both the primary phonon/heat signal and the simultaneously emitted scintillation light, which is absorbed in a separate silicon-on-sapphire light absorber, are measured with highly sensitive transition edge sensors operated at ~15mK. The unique combination of these sensors with the light element oxygen present in our target yields sensitivity to dark matter particle masses as low as 160MeV/c$^2$.Comment: 9 pages, 9 figure

Results on MeV-scale dark matter from a gram-scale cryogenic calorimeter operated above ground

Models for light dark matter particles with masses below 1 GeV/c$^2$ are a natural and well-motivated alternative to so-far unobserved weakly interacting massive particles. Gram-scale cryogenic calorimeters provide the required detector performance to detect these particles and extend the direct dark matter search program of CRESST. A prototype 0.5 g sapphire detector developed for the $\nu$-cleus experiment has achieved an energy threshold of $E_{th}=(19.7\pm 0.9)$ eV, which is one order of magnitude lower than previous results and independent of the type of particle interaction. The result presented here is obtained in a setup above ground without significant shielding against ambient and cosmogenic radiation. Although operated in a high-background environment, the detector probes a new range of light-mass dark matter particles previously not accessible by direct searches. We report the first limit on the spin-independent dark matter particle-nucleon cross section for masses between 140 MeV/c$^2$ and 500 MeV/c$^2$.Comment: 6 pages, 6 figures, v3: ancillary files added, v4: high energy spectrum (0.6-12keV) added to ancillary file

Limits on Dark Matter Effective Field Theory Parameters with CRESST-II

CRESST is a direct dark matter search experiment, aiming for an observation of nuclear recoils induced by the interaction of dark matter particles with cryogenic scintillating calcium tungstate crystals. Instead of confining ourselves to standard spin-independent and spin-dependent searches, we re-analyze data from CRESST-II using a more general effective field theory (EFT) framework. On many of the EFT coupling constants, improved exclusion limits in the low-mass region (< 3-4 GeV) are presented.Comment: 7 pages, 9 figure

Towards an automated data cleaning with deep learning in CRESST

The CRESST experiment employs cryogenic calorimeters for the sensitive measurement of nuclear recoils induced by dark matter particles. The recorded signals need to undergo a careful cleaning process to avoid wrongly reconstructed recoil energies caused by pile-up and read-out artefacts. We frame this process as a time series classification task and propose to automate it with neural networks. With a data set of over one million labeled records from 68 detectors, recorded between 2013 and 2019 by CRESST, we test the capability of four commonly used neural network architectures to learn the data cleaning task. Our best performing model achieves a balanced accuracy of 0.932 on our test set. We show on an exemplary detector that about half of the wrongly predicted events are in fact wrongly labeled events, and a large share of the remaining ones have a context-dependent ground truth. We furthermore evaluate the recall and selectivity of our classifiers with simulated data. The results confirm that the trained classifiers are well suited for the data cleaning task.Comment: 12 pages, 8 figures, 6 table

Lithium-Containing Crystals for Light Dark Matter Search Experiments

In the current direct dark matter search landscape, the leading experiments in the sub-GeV mass region mostly rely on cryogenic techniques which employ crystalline targets. One attractive type of crystals for these experiments is those containing lithium, due to the fact that 7Li is an ideal candidate to study spin-dependent dark matter interactions in the low mass region. Furthermore, 6Li can absorb neutrons, a challenging background for dark matter experiments, through a distinctive signature which allows the monitoring of the neutron flux directly on site. In this work, we show the results obtained with three different detectors based on LiAlO2, a target crystal never used before in cryogenic experiments

Cryogenic characterization of a LiAlO 2 crystal and new results on spin-dependent dark matter interactions with ordinary matter: CRESST Collaboration

In this work, a first cryogenic characterization of a scintillating LiAlO 2 single crystal is presented. The results achieved show that this material holds great potential as a target for direct dark matter search experiments. Three different detector modules obtained from one crystal grown at the Leibniz-Institut für Kristallzüchtung (IKZ) have been tested to study different properties at cryogenic temperatures. Firstly, two 2.8 g twin crystals were used to build different detector modules which were operated in an above-ground laboratory at the Max Planck Institute for Physics (MPP) in Munich, Germany. The first detector module was used to study the scintillation properties of LiAlO 2 at cryogenic temperatures. The second achieved an energy threshold of (213.02 ± 1.48) eV which allows setting a competitive limit on the spin-dependent dark matter particle-proton scattering cross section for dark matter particle masses between 350MeV/c2 and 1.50GeV/c2. Secondly, a detector module with a 373 g LiAlO 2 crystal as the main absorber was tested in an underground facility at the Laboratori Nazionali del Gran Sasso (LNGS): from this measurement it was possible to determine the radiopurity of the crystal and study the feasibility of using this material as a neutron flux monitor for low-background experiments. © 2020, The Author(s)