Caterina Strambio‐De‐Castillia

Accurate and robust 3D genome feature discovery from multiplexed DNA FISH

ArcFISH identifies 3D genome features from multiplexed DNA FISH data by modeling axis-specific measurement errors, showing reliable detection of chromatin loops, TAD boundaries, and A/B compartments.

SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

SnapFISH identifies chromatin loops from multiplexed DNA FISH data with high sensitivity and accuracy in mouse embryonic stem cells.

Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

This paper proposes tiered metadata specifications for light microscopy to improve data quality, reproducibility, and interoperability, inspired by genomic standards like Encode.

MethodsJ2: A Software Tool to Improve Microscopy Methods Reporting

MethodsJ2 is a software tool that collects metadata and generates text for the methods section of microscopy publications.

Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications

Micro-Meta App is an open-source tool that helps collect and organize microscopy metadata according to community standards, improving reproducibility and data sharing.

OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control

An algorithm-centric Monte Carlo method to empiricallyquantify motion type estimation uncertainty in single-particle tracking

The paper introduces a Monte Carlo method to quantify uncertainty in motion type estimation for single-particle tracking, addressing error propagation in bioimage analysis.

Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis

This paper proposes MIAPTE guidelines to standardize reporting of particle tracking experiments, enhancing data FAIRness and reproducibility.

Rapid isolation of functionally intact nuclei from the yeast Saccharomyces

This paper introduces a rapid method for isolating well-preserved yeast nuclei, enabling detailed structural and functional studies.