Kyle Harrington

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography

The paper describes a Kaggle challenge for particle picking in cryo-electron tomography, resulting in improved algorithms and highlighting the need for better annotation quality measures.

A generative AI framework for disease-specific lung microtissue bioengineering

This paper introduces a generative AI framework for designing and fabricating disease-specific lung microtissues using 3D imaging and bioprinting.

Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification

Polarity-JaM is an open-source image analysis tool for quantifying cell polarity, junctions, and morphology using deep learning and provides statistical analysis features.

Open-source Tools for CryoET Particle Picking Machine Learning Competitions

The paper introduces open-source tools for a machine learning competition focused on particle picking in cryo-electron tomography data.

Annotating CryoET Volumes: A Machine Learning Challenge

The paper introduces a phantom sample and annotated 3D volumes for a machine learning challenge to improve cryoET volume annotation.

Surforama: interactive exploration of volumetric data by leveraging 3D surfaces

Surforama enables interactive visualization and analysis of membrane proteins in cryo-ET data by rendering local densities on segmented surfaces and exporting results for further analysis.

A Connectome of the Male Drosophila Ventral Nerve Cord

Roughly 23 thousand traced neurons and 10 million TBars of the male Drosophila nerve cord, reconstructed from electron microscopy, typed, and queryable in neuPrint down to motor neurons.

RS-FISH: Precise, interactive, fast, and scalable FISH spot detection

RS-FISH detects FISH spots accurately and efficiently in 2D and 3D images, supporting applications like smFISH and spatial genomics.

PyZebrascope: an open-source platform for brain-wide neural activity imaging in zebrafish

PyZebrascope provides an open-source platform for whole-brain neural activity imaging in zebrafish using light-sheet microscopy, enabling high-throughput and stable data acquisition.

SNT: A Unifying Toolbox for Quantification of Neuronal Anatomy

SNT provides a unified framework for neuronal morphometry and single-cell connectomics analysis, integrating with Fiji and ImageJ to support tracing, quantification, and modeling of neuroanatomy.

Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy

This paper demonstrates the feasibility of 3D/4D light-sheet fluorescence microscopy for imaging mouse retinal pathology, revealing new features in the OIR model and highlighting distorted morphology from flat-mounting.

Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish

The paper presents a multi-sample imaging, processing, and analysis platform for studying vascular growth in zebrafish over time.