Hari Shroff
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View article: The CENP-A chaperone complex spatially organizes centromeres
The CENP-A chaperone complex spatially organizes centromeres Open
Centromeres, defined by CENP-A-containing nucleosomes, direct the assembly of kinetochores for spindle attachment. In mitosis, CENP-A and the constitutive centromere-associated network (CCAN) of the inner kinetochore are arranged into bipa…
View article: Observing biological spatio-angular structures and dynamics with statistical image reconstruction and polarized fluorescence microscopy
Observing biological spatio-angular structures and dynamics with statistical image reconstruction and polarized fluorescence microscopy Open
Understanding molecular orientation and density distributions is essential for exploring biological structure and function. Polarized fluorescence microscopy (PFM) provides insights into molecular architecture but struggles to resolve thre…
View article: HD2Net: a deep learning framework for simultaneous denoising and deaberration in fluorescence microscopy
HD2Net: a deep learning framework for simultaneous denoising and deaberration in fluorescence microscopy Open
Fluorescence microscopy is essential for biological research, offering high-contrast imaging of microscopic structures. However, the quality of these images is often compromised by optical aberrations and noise, particularly in low signal-…
View article: Resolution in super-resolution microscopy – facts, artifacts, technological advancements and biological applications
Resolution in super-resolution microscopy – facts, artifacts, technological advancements and biological applications Open
Super-resolution microscopy (SRM) has undeniable potential for scientific discovery, yet still presents many challenges that hinder its widespread adoption, including technical trade-offs between resolution, speed and photodamage, as well …
View article: Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope
Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope Open
Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations in biological samples, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a p…
View article: HD2Net: A Deep Learning Framework for Simultaneous Denoising and Deaberration in Fluorescence Microscopy
HD2Net: A Deep Learning Framework for Simultaneous Denoising and Deaberration in Fluorescence Microscopy Open
Fluorescence microscopy is essential for biological research, offering high-contrast imaging of microscopic structures. However, the quality of these images is often compromised by optical aberrations and noise, particularly in low signal-…
View article: Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy
Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy Open
Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing ima…
View article: Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity
Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity Open
Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation nonuniformly to secure against the possibility that favorabl…
View article: Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells
Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells Open
Stereocilia are unidirectional F-actin-based cylindrical protrusions on the apical surface of inner ear hair cells and function as biological mechanosensors of sound and acceleration. Development of functional stereocilia requires motor ac…
View article: Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore
Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore Open
All multicellular systems produce and dynamically regulate extracellular matrices (ECM) that play important roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to…
View article: Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells
Live-cell single-molecule fluorescence microscopy for protruding organelles reveals regulatory mechanisms of MYO7A-driven cargo transport in stereocilia of inner ear hair cells Open
Stereocilia are unidirectional F-actin-based cylindrical protrusions on the apical surface of inner ear hair cells and function as biological mechanosensors of sound and acceleration. Development of functional stereocilia requires motor ac…
View article: Phase-diversity-based wavefront sensing for fluorescence microscopy
Phase-diversity-based wavefront sensing for fluorescence microscopy Open
Fluorescence microscopy is an invaluable tool in biology, yet its performance is compromised when the wavefront of light is distorted due to optical imperfections or the refractile nature of the sample. Such optical aberrations can dramati…
View article: Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity
Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity Open
Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation non-uniformly to secure against the possibility that favorab…
View article: Cell division machinery drives cell-specific gene activation during differentiation in <i>Bacillus subtilis</i>
Cell division machinery drives cell-specific gene activation during differentiation in <i>Bacillus subtilis</i> Open
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components…
View article: Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM)
Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM) Open
Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view lig…
View article: Prediction of Cellular Identities from Trajectory and Cell Fate Information
Prediction of Cellular Identities from Trajectory and Cell Fate Information Open
Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovativ…
View article: Live-cell imaging powered by computation
Live-cell imaging powered by computation Open
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. We focus here on computational methods that promise to boost live-cell fluorescence microscopy, …
View article: Phase diversity-based wavefront sensing for fluorescence microscopy
Phase diversity-based wavefront sensing for fluorescence microscopy Open
Fluorescence microscopy is an invaluable tool in biology, yet its performance is compromised when the wavefront of light is distorted due to optical imperfections or the refractile nature of the sample. Such optical aberrations can dramati…
View article: Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy
Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy Open
Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing ima…
View article: Cell division machinery drives cell-specific gene activation during bacterial differentiation
Cell division machinery drives cell-specific gene activation during bacterial differentiation Open
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components…
View article: Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches.
Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches. Open
Phase diversity is a widefield aberration correction method that uses multiple images to estimate the phase aberration at the pupil plane of an imaging system by solving an optimization problem. This estimated aberration can then be used t…
View article: Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches
Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches Open
Phase diversity is a widefield aberration correction method that uses multiple images to estimate the phase aberration at the pupil plane of an imaging system by solving an optimization problem. This estimated aberration can then be used t…
View article: Label‐free cleared tissue microscopy and machine learning for <scp>3D</scp> histopathology of biomaterial implants
Label‐free cleared tissue microscopy and machine learning for <span>3D</span> histopathology of biomaterial implants Open
Tissue clearing of whole intact organs has enhanced imaging by enabling the exploration of tissue structure at a subcellular level in three‐dimensional space. Although clearing and imaging of the whole organ have been used to study tissue …