imputation

Using regularized regression and biological covariation to impute missing values in quantitative proteomics

The paper introduces a method to impute missing proteomics data using regularized regression and biological covariation, achieving high accuracy across multiple measurement modalities.

Open Raman Microscopy (ORM): A Modular Hardware and Software Framework for Accessible Raman Imaging

The paper introduces an open-source Raman microscopy framework with modular hardware and software for accessible chemical imaging across various applications.

BMDD: A Probabilistic Framework for Accurate Imputation of Zero-inflated Microbiome Sequencing Data

BMDD improves microbiome data imputation by modeling bimodal abundance distributions, outperforming existing methods in accuracy and uncertainty estimation.

A genetically encoded marker for imaging membranes of Plasmodium

The paper introduces FLUMMI, a peptide marker for imaging internal membranes in Plasmodium without affecting viability, and shows its compatibility with live-cell and expansion microscopy.

Real-time, High-throughput Super-resolution Microscopy via Panoramic Integration

This paper introduces SPI, a super-resolution microscopy technique that enables real-time, high-throughput imaging with minimal post-processing.

Deep-learning-assisted SICM for enhanced real-time imaging of nanoscale biological dynamics

This paper introduces a deep-learning-assisted framework to enhance real-time SICM imaging by reducing scan time while maintaining image quality and structural integrity.

Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development

Combining 99-gene smFISH across 48,225 cells with scRNA-seq of 26,009 cells maps 21 spatial expression domains and imputes 74,464 genes in early tetraploid wheat spikes.

Parallel frequency-multiplexed aberration measurement for widefield fluorescence microscopy

This paper introduces PFAM and PFAM-SIFT methods for parallel aberration measurement in widefield fluorescence microscopy, enabling accurate correction of spatially varying aberrations in complex samples.

Quality-control Normalization of Fluorescence Microscopy Morphometry and Colocalization Measurements for Improved Accuracy and Cross-instrument Reproducibility

This paper introduces a normalization workflow for fluorescence microscopy data using quality-control metrics to improve measurement accuracy and cross-instrument reproducibility.

Single-aperture SLAM microscopy with amplitude-tailored vector beams

This paper introduces a single-aperture SLAM microscope using vector beams to achieve sub-diffraction-limited resolution in living tissue.

Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy.

The paper introduces miOPM, a reconfigurable LSFM platform that enables high-resolution imaging across multiple spatial scales and refractive indices.

Chimeric Reference Panels for Genomic Imputation

Retriever enables genotype imputation without external reference panels by constructing chimeric reference panels from target samples, achieving over 95% accuracy across diverse species.

A switch from TE-like heterochromatin to euchromatin underlies activation of protein storage genes in maize endosperm

The paper identifies TE-like methylated genes in maize endosperm that are demethylated and highly expressed, revealing a switch from heterochromatin to euchromatin that activates protein storage genes.

Programmable orthogonal and rapid DNA strand displacement for fluidic-exchange-free highly multiplexed fluorescent imaging

This paper introduces a method for high-plex fluorescent imaging using DNA strand displacement without fluidic exchange, achieving 25-plex RNA imaging in fixed cells.

Interferometric Image Scanning Microscopy for label-free imaging at 120 nm resolution inside live cells

This paper introduces iISM, a label-free imaging technique with 120 nm resolution for live cell imaging, reducing photodamage and enabling long-term observation of subcellular structures.

Two-Dimensional Nonlinear Structured Illumination Microscopy with rsEGFP2

The paper demonstrates 2D nonlinear structured illumination microscopy (NSIM) using rsEGFP2 to achieve sub-80 nm resolution for live-cell actin imaging.

SIMple: A fibre-based platform for accessible structured illumination microscopy

The paper introduces a fibre-based structured illumination microscopy (SIM) system that simplifies setup and improves resolution without specialized optics.

CytoVI: Deep generative modeling of antibody-based single cell technologies

CytoVI is a deep generative model for antibody-based single cell technologies that improves integration, imputation, and analysis across different platforms and antibody panels.

A framework to enhance the Signal-to-Noise Ratio for quantitative fluorescence microscopy

This paper develops a framework to enhance the signal-to-noise ratio in quantitative fluorescence microscopy by optimizing camera parameters and microscope settings.

A large 3D-printed integrated lens-biprism element enhances contrast in transmission stereomicroscopy

The paper introduces a 3D-printed lens-biprism element that improves image contrast in stereomicroscopy by enhancing illumination uniformity.

Incubator-Free Organoid Culture in a Sealed Recirculatory System

This paper introduces a sealed recirculatory system for organoid culture that eliminates the need for CO2 incubators and enables continuous live imaging and metabolic viability.

Scvi-hub: an actionable repository for model-driven single cell analysis

Scvi-hub provides a platform for sharing and analyzing single-cell omics datasets using pre-trained models, enabling efficient tasks like visualization and annotation with reduced computational demands.

An Enhanced Mountain Climbing Search Algorithm to Enable Fast and Accurate Autofocusing in High Resolution Fluorescence Microscopy

This paper introduces an enhanced mountain climbing search algorithm for fast and accurate autofocus in high-resolution fluorescence microscopy, achieving up to 200-fold improvement in precision over existing methods.

SpaIM: Single-cell Spatial Transcriptomics Imputation via Style Transfer

SpaIM improves spatial transcriptomics by imputing missing gene expressions using scRNA-seq data, outperforming 12 existing methods across 53 datasets.

Pedigree-based genome-wide imputation using a low-density amplicon panel for the highly polymorphic Pacific oyster Crassostrea (Magallana) gigas

The paper demonstrates genome-wide imputation using a low-density amplicon panel in Pacific oysters to reduce genotyping costs and improve selective breeding.

Acoustic Transparency Enabling Functional Ultrasound Imaging Through Mouse and Human Skulls

This paper develops an acoustic transparency method using a chelating agent to enable functional ultrasound imaging through mouse and human skulls.

Magellon - an extensible platform for cryo-EM data visualization, management, and processing

Magellon provides a flexible and scalable cryo-EM platform with microservices architecture for data management, processing, and visualization.

Cleared tissue dual-view oblique plane microscopy

This paper introduces a dual-view oblique plane microscope for high-resolution imaging of thick cleared tissue samples across multiple species.

Super-resolved live imaging of thick biological samples with 3D Random Illumination Microscopy (3D-RIM)

This paper introduces 3D-RIM, a method that achieves super-resolved volume imaging of thick live specimens with high contrast and resolution across multiple microns.

Pan-ASLM: a high-resolution and large-field-of-view light sheet microscope for Expansion Microscopy

The paper introduces pan-ASLM, a light sheet microscope optimized for expansion microscopy, achieving higher speed, larger field of view, and better resolution than standard confocal microscopes.