K. W. Dunn

A Quantitative Metric of Confidence For Segmentation of Nuclei in Large Spatially Variable Image Volumes

The paper introduces a confidence metric for nuclei segmentation in large spatially variable image volumes, showing it correlates with segmentation quality and F1 scores.

3D Ground Truth Annotations of Nuclei in 3D Microscopy Volumes

The paper provides 3D microscopy volumes with partial manual annotations and synthetically generated volumes for training segmentation methods.

3D CentroidNet: Nuclei Centroid Detection With Vector Flow Voting

This paper introduces a 3D nuclei centroid detection method using vector flow voting, achieving better performance than existing methods on real microscopy data.

NISNet3D: Three-Dimensional Nuclear Synthesis and Instance Segmentation for Fluorescence Microscopy Images

NISNet3D is a deep learning model for 3D nuclear segmentation in fluorescence microscopy images, trained on synthetic data and compared to eight existing methods.

DINAVID: A Distributed and Networked Image Analysis System for Volumetric Image Data

DINAVID provides a cloud-based system for remote 3D microscopy image analysis and visualization, designed to handle large datasets and improve accessibility.

An Ensemble Learning and Slice Fusion Strategy for Three-Dimensional Nuclei Instance Segmentation

This paper introduces EMR-CNN, a 3D nuclei segmentation method that avoids ground truth annotations and uses ensemble learning and slice fusion for efficient and accurate results.

Integrated cytometry with machine learning applied to high-content imaging of human kidney tissue for in-situ cell classification and neighborhood analysis

The paper introduces VTEA, a software tool that integrates machine learning and cytometry analysis for high-content imaging of human kidney tissue to classify cells and analyze their spatial neighborhoods.

A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: The Kidney Precision Medicine Project

The paper describes a pipeline for generating 3D molecular atlases of human kidney biopsies using multi-OMICS and imaging technologies, emphasizing quality control and reproducibility across institutions.

In situ classification of cell types in human kidney tissue using 3D nuclear staining

This paper develops a deep learning method using 3D nuclear staining to classify cell types in human kidney tissue without requiring specific markers.

PIE-FLIM measurements of two different FRET-based biosensor activities in the same living cells

The paper demonstrates PIE-FLIM for simultaneous measurement of two FRET-based biosensor activities in living cells.

Longitudinal Intravital Imaging of Biosensor-labeled In Situ Islet Beta Cells

This study uses intravital imaging of biosensor-labeled beta cells to monitor ROS dynamics in vivo during diabetes-related stress.