arXiv subjects

Shantanu Singh

Publications and source records attributed to Shantanu Singh.

35 records · Page 2Linked to original sources

arXiv2024

Reproducible image-based profiling with Pycytominer

Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To process these single-cells for downstream applications, we present Pycytominer, a user-friendly, open-source python package that implements the bioinformatics steps, known as image-based profiling. We demonstrate Pycytominers usefulness in a machine learning project to predict nuisance compounds that cause undesirable cell injuries.

q-bio.QM↗

arXiv2024

Bifunctional Noble Metal-free Ternary Chalcogenide Electrocatalysts for Overall Water Splitting

Hydrogen has been identified as a clean, zero carbon, sustainable, and promising energy source for the future, and electrochemical water splitting for hydrogen production is an emission-free, efficient energy conversion technology. A major limitation of this approach is the unavailability of efficient, abundant, inexpensive catalysts, which prompts the need for new catalytic materials. Here, we report the synthesis and electrocatalytic properties of a novel transition metal-based ternary chalcogenide family, LaMS$_3$ (M = Mn, Fe, Co, Ni). Powder X-ray diffraction confirms the phase purity of these materials, while composition analysis using energy dispersive spectroscopy (EDS) confirms the presence of the stoichiometric ratio of elements in these compounds. X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS) were used to study the chemical states on the surface and in bulk, respectively. These materials exhibit bifunctional catalytic activity towards the two half-reactions of the water-splitting process, with LaNiS$_3$ being the most active material for both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). The LaMS$_3$ compounds show long-term stability with negligible change in the overpotential at a constant current density of 10 mA cm$^{-2}$ over 18 hours of measurements. As compared to the corresponding ternary oxides, the LaMS$_3$ materials exhibit higher activity and significantly lower Tafel slopes. The ability to catalyze both half-reactions of water electrolysis makes these materials promising candidates for bifunctional catalysts and presents a new avenue to search for high-efficiency electrocatalysts for water splitting.

physics.chem-ph↗

arXiv2024

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other -omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded the ability of Cell Painting to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.

q-bio.SC↗

arXiv2024

Giant Modulation of Refractive Index from Picoscale Atomic Displacements

Structural disorder has been shown to enhance and modulate magnetic, electrical, dipolar, electrochemical, and mechanical properties of materials. However, the possibility of obtaining novel optical and optoelectronic properties from structural disorder remains an open question. Here, we show unambiguous evidence of disorder in the form of anisotropic, picoscale atomic displacements modulating the refractive index tensor and resulting in the giant optical anisotropy observed in BaTiS$_3$, a quasi-one-dimensional hexagonal chalcogenide. Single crystal X-ray diffraction studies reveal the presence of antipolar displacements of Ti atoms within adjacent TiS$_6$ chains along the c-axis, and three-fold degenerate Ti displacements in the a-b plane. $^{47/49}$Ti solid-state NMR provides additional evidence for those Ti displacements in the form of a three-horned NMR lineshape resulting from a low symmetry local environment around Ti atoms. We used scanning transmission electron microscopy to directly observe the globally disordered Ti a-b plane displacements and find them to be ordered locally over a few unit cells. First-principles calculations show that the Ti a-b plane displacements selectively reduce the refractive index along the ab-plane, while having minimal impact on the refractive index along the chain direction, thus resulting in a giant enhancement in the optical anisotropy. By showing a strong connection between structural disorder with picoscale displacements and the optical response in BaTiS$_3$, this study opens a pathway for designing optical materials with high refractive index and functionalities such as large optical anisotropy and nonlinearity.

cond-mat.mtrl-sci↗

arXiv2024

Molten flux growth of single crystals of quasi-1D hexagonal chalcogenide BaTiS3

BaTiS3, a quasi-1D complex chalcogenide, has gathered considerable scientific and technological interest due to its giant optical anisotropy and electronic phase transitions. However, the synthesis of high-quality BaTiS3 crystals, particularly those featuring crystal sizes of millimeters or larger, remains a challenge. Here, we investigate the growth of BaTiS3 crystals utilizing a molten salt flux of either potassium iodide, or a mixture of barium chloride and barium iodide. The crystals obtained through this method exhibit a substantial increase in volume compared to those synthesized via the chemical vapor transport method, while preserving their intrinsic optical and electronic properties. Our flux growth method provides a promising route towards the production of high-quality, large-scale single crystals of BaTiS3, which will greatly facilitate advanced characterizations of BaTiS3 and its practical applications that require large crystal dimensions. Additionally, our approach offers an alternative synthetic route for other emerging complex chalcogenides.

cond-mat.mtrl-sci↗

arXiv2024

Understanding Biology in the Age of Artificial Intelligence

Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research - protein structure prediction and single cell RNA-sequencing - we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems.

cs.AI↗

arXiv2024

Infrared Optical Anisotropy in Quasi-1D Hexagonal Chalcogenide BaTiSe3

Polarimetric infrared detection bolsters IR thermography by leveraging the polarization of light. Optical anisotropy, i.e., birefringence and dichroism, can be leveraged to achieve polarimetric detection. Recently, giant optical anisotropy was discovered in quasi-1D narrow-bandgap hexagonal perovskite sulfides, A1+xTiS3, specifically BaTiS3[1,2] and Sr9/8TiS3[3,4]. In these materials, the critical role of atomic-scale structure modulations[4,5] in the unconventional electrical[5,6], optical[7,8], and thermal[7,9] properties raises the broader question of other materials that belong to this family. To address this issue, for the first time, we synthesized high-quality single crystals of a largely unexplored member of the A1+xTiX3 (X = S, Se) family, BaTiSe3. Single-crystal X-ray diffraction determined the room-temperature structure with the P31c space group, which is a superstructure of the earlier reported[10] P63/mmc structure. The crystal structure of BaTiSe3 features antiparallel c-axis displacements similar to BaTiS3,[2] but is of lower symmetry. Polarization-resolved Raman and Fourier transform infrared (FTIR) spectroscopy were used to characterize the optical anisotropy of BaTiSe3, whose refractive index along the ordinary (perpendicular to c) and extraordinary (parallel to c) optical axes was quantitatively determined by combining ellipsometry studies with FTIR. With a giant birefringence Δn~0.9, BaTiSe3 emerges as a new candidate for miniaturized birefringent optics for mid-wave infrared to long-wave infrared imaging.

cond-mat.mtrl-sci↗

arXiv2024

Cell Painting Gallery: an open resource for image-based profiling

Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical perturbations. The Cell Painting assay is the most popular imaged-based profiling assay wherein six small-molecule dyes label eight cellular compartments and thousands of measurements are made, describing quantitative traits such as size, shape, intensity, and texture within the nucleus, cytoplasm, and whole cell (Cimini et al., 2023). We have created the Cell Painting Gallery, a publicly available collection of Cell Painting datasets, with granular dataset descriptions and access instructions. It is hosted by AWS on the Registry of Open Data (RODA). As of January 2024, the Cell Painting Gallery holds 656 terabytes (TB) of image and associated numerical data. It includes the largest publicly available Cell Painting dataset, in terms of perturbations tested (Joint Undertaking for Morphological Profiling or JUMP (Chandrasekaran et al., 2023)), along with many other canonical datasets using Cell Painting, close derivatives of Cell Painting (such as LipocyteProfiler (Laber et al., 2023) and Pooled Cell Painting (Ramezani et al., 2023)).

q-bio.QM↗

arXiv2023

A hybrid pulsed laser deposition approach to grow thin films of chalcogenides

Vapor-pressure mismatched materials such as transition metal chalcogenides have emerged as electronic, photonic, and quantum materials with scientific and technological importance. However, epitaxial growth of vapor-pressure mismatched materials are challenging due to differences in the reactivity, sticking coefficient, and surface adatom mobility of the mismatched species constituting the material, especially sulfur containing compounds. Here, we report a novel approach to grow chalcogenides - hybrid pulsed laser deposition - wherein an organosulfur precursor is used as a sulfur source in conjunction with pulsed laser deposition to regulate the stoichiometry of the deposited films. Epitaxial or textured thin films of sulfides with variety of structure and chemistry such as alkaline metal chalcogenides, main group chalcogenides, transition metal chalcogenides and chalcogenide perovskites are demonstrated, and structural characterization reveal improvement in thin film crystallinity, and surface and interface roughness compared to the state-of-the-art. The growth method can be broadened to other vapor-pressure mismatched chalcogenides such as selenides and tellurides. Our work opens up opportunities for broader epitaxial growth of chalcogenides, especially sulfide-based thin film technological applications.

cond-mat.mtrl-sci↗

arXiv2023

Photoconductive Effects in Single Crystals of BaZrS$_3$

Chalcogenide perovskites, such as BaZrS$_3$, are emerging semiconductors with potential for high photovoltaic power conversion efficiency. The role of defects in the efficiency of the generation and collection of photo-excited carriers has not been experimentally investigated extensively. We study the effect of processing-induced defects on the photoconductive properties of single crystals of BaZrS$_3$. We achieved ohmic contacts to single crystals of BaZrS$_3$ and observed positive surface photovoltage, which is typically observed in p-type semiconductors. However, mechanical polishing of BaZrS$_3$ to remove the surface oxide leads to dense deformation grain boundaries and leads to trap-dominated photoconductive response. In comparison, ohmic contacts achieved in cleaved crystals leave fewer deformation defects and greatly improve optoelectronic properties. Defect-controlled crystal growth and contact fabrication are potentially limiting factors for achieving high photon-to-excited electron conversion efficiency in BaZrS$_3$.

physics.app-ph↗

arXiv2023

Colossal optical anisotropy from atomic-scale modulations

In modern optics, materials with large birefringence (Δn, where n is the refractive index) are sought after for polarization control (e.g. in wave plates, polarizing beam splitters, etc.), nonlinear optics and quantum optics (e.g. for phase matching and production of entangled photons), micromanipulation, and as a platform for unconventional light-matter coupling, such as Dyakonov-like surface polaritons and hyperbolic phonon polaritons. Layered "van der Waals" materials, with strong intra-layer bonding and weak inter-layer bonding, can feature some of the largest optical anisotropy; however, their use in most optical systems is limited because their optic axis is out of the plane of the layers and the layers are weakly attached, making the anisotropy hard to access. Here, we demonstrate that a bulk crystal with subtle periodic modulations in its structure -- Sr9/8TiS3 -- is transparent and positive-uniaxial, with extraordinary index n_e = 4.5 and ordinary index n_o = 2.4 in the mid- to far-infrared. The excess Sr, compared to stoichiometric SrTiS3, results in the formation of TiS6 trigonal-prismatic units that break the infinite chains of face-shared TiS6 octahedra in SrTiS3 into periodic blocks of five TiS6 octahedral units. The additional electrons introduced by the excess Sr subsequently occupy the TiS6 octahedral blocks to form highly oriented and polarizable electron clouds, which selectively boost the extraordinary index n_e and result in record birefringence (Δn > 2.1 with low loss). The connection between subtle structural modulations and large changes in refractive index suggests new categories of anisotropic materials and also tunable optical materials with large refractive-index modulation and low optical losses.

physics.optics↗

arXiv2023

Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images

Various strategies for label-scarce object detection have been explored by the computer vision research community. These strategies mainly rely on assumptions that are specific to natural images and not directly applicable to the biological and biomedical vision domains. For example, most semi-supervised learning strategies rely on a small set of labeled data as a confident source of ground truth. In many biological vision applications, however, the ground truth is unknown and indirect information might be available in the form of noisy estimations or orthogonal evidence. In this work, we frame a crucial problem in spatial transcriptomics - decoding barcodes from In-Situ-Sequencing (ISS) images - as a semi-supervised object detection (SSOD) problem. Our proposed framework incorporates additional available sources of information into a semi-supervised learning framework in the form of privileged information. The privileged information is incorporated into the teacher's pseudo-labeling in a teacher-student self-training iteration. Although the available privileged information could be data domain specific, we have introduced a general strategy of pseudo-labeling enhanced by privileged information (PLePI) and exemplified the concept using ISS images, as well on the COCO benchmark using extra evidence provided by CLIP.

cs.CV↗

arXiv2022

Unconventional Charge-density-wave Order in a Dilute d-band Semiconductor

Electron-lattice coupling effects in low dimensional materials give rise to charge density wave (CDW) order and phase transitions. These phenomena are critical ingredients for superconductivity and predominantly occur in metallic model systems such as doped cuprates, transition metal dichalcogenides, and more recently, in Kagome lattice materials. However, CDW in semiconducting systems, specifically at the limit of low carrier concentration region, is uncommon. Here, we combine electrical transport, synchrotron X-ray diffraction and optical spectroscopy to discover CDW order in a quasi-one-dimensional (1D), dilute d-band semiconductor, BaTiS3, which suggests the existence of strong electron-phonon coupling. The CDW state further undergoes an unusual transition featuring a sharp increase in carrier mobility. Our work establishes BaTiS3 as a unique platform to study the CDW physics in the dilute filling limit to explore novel electronic phases.

cond-mat.mtrl-sci↗

arXiv2022

Orientation Controlled Anisotropy in Single Crystals of Quasi-1D BaTiS3

Low-dimensional materials with chain-like (one-dimensional) or layered (twodimensional) structures are of significant interest due to their anisotropic electrical, optical, thermal properties. One material with chain-like structure, BaTiS3 (BTS), was recently shown to possess giant in-plane optical anisotropy and glass-like thermal conductivity. To understand the origin of these effects, it is necessary to fully characterize the optical, thermal, and electronic anisotropy of BTS. To this end, BTS crystals with different orientations (aand c-axis orientations) were grown by chemical vapor transport. X-ray absorption spectroscopy (XAS) was used to characterize the local structure and electronic anisotropy of BTS. Fourier transform infrared (FTIR) reflection/transmission spectra show a large inplane optical anisotropy in the a-oriented crystals, while the c-axis oriented crystals were nearly isotropic in-plane. BTS platelet crystals are promising uniaxial materials for IR optics with their optic axis parallel to the c-axis. The thermal conductivity measurements revealed a thermal anisotropy of ~4.5 between the c- and a-axis. Time-domain Brillouin scattering showed that the longitudinal sound speed along the two axes is nearly the same suggesting that the thermal anisotropy is a result of different phonon scattering rates.

cond-mat.mtrl-sci↗

arXiv2021

Epitaxial Thin Films of a Chalcogenide Perovskite

Chalcogenide perovskites have emerged as a new class of electronic materials, but fundamental properties and applications of chalcogenide perovskites remain limited by the lack of high quality epitaxial thin films. We report epitaxial thin film growth of BaZrS3, a prototypical chalcogenide, by pulsed laser deposition. X-ray diffraction studies show that the films are strongly textured out of plane and have a clear in-plane epitaxial relationship with the substrate. Electron microscopy studies confirm the presence of epitaxy for the first few layers of the film at the interface, even though away from the interface the films are polycrystalline with a large number of extended defects suggesting the potential for further improvement in growth. X-Ray reflectivity and atomic force microscopy show smooth film surfaces and interfaces between the substrate and the film. The films show strong light absorption near the band edge and photoluminescence in the visible region. The photodetector devices show fast and efficient photo response with the highest ON/OFF ratio reported for BaZrS3 films thus far. Our study opens up opportunities to realize epitaxial thin films, heterostructures, and superlattices of chalcogenide perovskites to probe fundamental physical phenomena and the resultant electronic and photonic device technologies.

cond-mat.mtrl-sci↗

arXiv2019

Smart Laptop Bag with Machine Learning for Activity Recognition

In todays world of smart living, the smart laptop bag, presented in this paper, provides a better solution to keep track of our precious possessions and monitoring them in real time. As the world moves towards a much tech-savvy direction, the novel laptop bag discussed here facilitates the user to perform location tracking, ambiance monitoring, user-state monitoring etc. in one device. The innovative design uses cloud computing and machine learning algorithms to monitor the health of the user and many parameters of the bag. The emergency alert system in this bag could be trained to send appropriate notifications to emergency contacts of the user, in case of abnormal health conditions or theft of the bag. The experimental smart laptop bag uses deep neural network, which was trained and tested over the various parameters from the bag and produces above 95% accurate results.

cs.OH↗

arXiv2014

Analysis of Femoral Components of Cemented Total Hip- Arthroplasty

In cemented Total Hip Arthroplasty (THA), material chosen for femoral stem and cross section of stem itself, proved to be critical parameters for, stress distribution in the femoral components, interfacial stresses and micro movements. Titanium alloy (Ti6Al4V), when used as a material for femoral stem, recorded large displacement as compared to Chromium alloy (CoCrMo) stems. This large displacement in case of Ti6Al4V caused the stem to bend inside the cement mantle, thus destroying it. Thus, CoCrMo proved to be a better in cemented THA. Failure in THA may occur at cement-stem or cement-bone interface, thus interfacial stresses and micro movements were analysed in the present study. Comparison between trapezium and circular cross section showed that, femoral stem with trapezium cross section underwent lesser amount of sliding and debonding, at both interfaces, as compared to circular cross section. Moreover, trapezium cross section also generated lower peak stresses in femoral stem and cortical femur. The present study also took into account, effect of diameter of femur head. A 36mm diameter femur head generated lower peak stress in acetabulum liner and arrested dislocation. Metallic femur head was coupled with a liner made of cross linked polyethylene (XLPE). This material experiences almost negligible wear when compared to typical metallic and polyethylene liners, and unlike metallic liner, it is non-carcinogenic.

physics.med-ph↗