Logan A. Walker

A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging

The paper introduces a parallelly distributed microscope and software system for high-throughput multispectral 3D imaging with high resolution and data throughput.

A browser-based platform for storage, visualization, and analysis of large-scale 3D images in HPC environments

The paper develops a platform for storing, visualizing, and analyzing large-scale 3D images in HPC environments using a scalable storage format and web-based annotation tools.

Artifact-Minimized High-Ratio Image Compression with Preserved Analysis Fidelity

This paper develops a compression method that achieves high compression ratios with minimal visual and quantitative errors for single-molecule imaging data.

A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications

This study compares lossless compression methods for microscopy data, recommending BLOSC with ZSTD for optimal compression ratios across various conditions.

OPTIMIZED NEURON TRACING USING POST HOC REANALYSIS

The paper introduces nCorrect, an algorithm that improves neuron tracing by reanalyzing existing traces to produce more physiologically-relevant reconstructions using a 4D minimization algorithm and a new similarity metric.

Profiling neurons surrounding subcellular-scale carbon fiber electrode tracts enables modeling recorded signals

The paper localizes neurons around subcellular-scale carbon fiber electrodes and shows their placement affects spike sorting reliability.

nGauge: Integrated and extensible neuron morphology analysis in Python

nGauge provides an extensible Python toolkit for analyzing neuron morphology data, improving data compatibility and enabling advanced analysis and visualization.

Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations

This study compares bulk and single-cell RNAseq for identifying differentially expressed genes in adult hippocampal NSCs, finding single-cell methods miss high-fold-change genes but can be optimized for in vivo use.

Bitbow: a digital format of Brainbow enables highly efficient neuronal lineage tracing and morphology reconstruction in single brains

Unsupervised Neural Tracing in Densely Labeled Multispectral Brainbow Images

This paper introduces an unsupervised method for tracing neurons in multispectral Brainbow images, achieving more accurate results than existing methods by reducing segmentation and continuity errors.

The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and a multi-informatic analysis paradigm

The paper uses targeted scRNA-seq and multi-informatic analysis to characterize neural differentiation in Drosophila brain neuroblast lineages and provides a visualization tool for gene function curation.

Light microscopy based approach for mapping connectivity with molecular specificity

The paper introduces a light microscopy method called spectral connectomics to map neural connectivity with molecular specificity by combining genetic labeling and immunostaining.

TraceMontage: a Method for Merging Multiple Independent Neuronal Traces

TraceMontage merges multiple neuronal traces into a single result, improving accuracy and speed for densely labeled samples.