Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

(2019) Juan C. Caicedo et al.   CYTOMETRY PART A

Three-dimensional GPU-accelerated active contours for automated localization of cells in large images

(2019) Mahsa Lotfollahi et al.   PLoS One

Automated Classification of Apoptosis in Phase Contrast Microscopy Using Capsule Network

(2019) Aryan Mobiny et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Algorithms for Fitting the Constrained Lasso

(2018) Brian R. Gaines et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

A Guide to Single-Cell Transcriptomics in Adult Rodent Brain: The Medium Spiny Neuron Transcriptome Revisited

(2018) Hanson Ho et al.   Frontiers in Cellular Neuroscience

Next generation histology methods for three-dimensional imaging of fresh and archival human brain tissues

(2018) Hei Ming Lai et al.   Nature Communications

U-Net: deep learning for cell counting, detection, and morphometry

(2018) Thorsten Falk et al.   NATURE METHODS

Development of a systems-based in situ multiplex biomarker screening approach for the assessment of immunopathology and neural tissue plasticity in male rats after traumatic brain injury

(2017) Tanya Bogoslovsky et al.   JOURNAL OF NEUROSCIENCE RESEARCH

When machine vision meets histology: A comparative evaluation of model architecture for classification of histology sections

(2017) Cheng Zhong et al.   MEDICAL IMAGE ANALYSIS

Whole cell maps chart a course for 21st-century cell biology

(2017) Rick Horwitz et al.   SCIENCE

Comparative transcriptome analysis in induced neural stem cells reveals defined neural cell identities in vitro and after transplantation into the adult rodent brain

(2016) Anna-Lena Hallmann et al.   Stem Cell Research

Analysis of the brain mural cell transcriptome

(2016) Liqun He et al.   Scientific Reports

Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors

(2015) Murad Megjhani et al.   BIOINFORMATICS

Recent developments in multiplexing techniques for immunohistochemistry

(2015) Angela R Dixon et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Acute Response of the Hippocampal Transcriptome Following Mild Traumatic Brain Injury After Controlled Cortical Impact in the Rat

(2015) Babru B. Samal et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

Deep learning

(2015) Yann LeCun et al.   NATURE

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving fluorophores by unmixing multispectral fluorescence tomography with independent component analysis

(2014) Huangsheng Pu et al.   PHYSICS IN MEDICINE AND BIOLOGY

Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python

(2014) Nicolas Rey-Villamizar et al.   Frontiers in Neuroinformatics

Serial two-photon tomography for automated ex vivo mouse brain imaging

(2012) Timothy Ragan et al.   NATURE METHODS

Digital Transplantation Pathology: Combining Whole Slide Imaging, Multiplex Staining and Automated Image Analysis

(2011) K. Isse et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Robust, globally consistent and fully automatic multi-image registration and montage synthesis for 3-D multi-channel images

(2011) C.-L. TSAI et al.   JOURNAL OF MICROSCOPY

Regression shrinkage and selection via the lasso: a retrospective

(2011) Robert Tibshirani   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Improved Automatic Detection and Segmentation of Cell Nuclei in Histopathology Images

(2009) Y. Al-Kofahi et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Associative image analysis: A method for automated quantification of 3D multi-parameter images of brain tissue

(2008) Christopher S. Bjornsson et al.   JOURNAL OF NEUROSCIENCE METHODS