A survey of methods for 3D histology reconstruction

J Pichat, JE Iglesias, T Yousry, S Ourselin… - Medical image analysis, 2018 - Elsevier
Histology permits the observation of otherwise invisible structures of the internal topography
of a specimen. Although it enables the investigation of tissues at a cellular level, it is invasive …

Impairment of glycolysis-derived l-serine production in astrocytes contributes to cognitive deficits in Alzheimer's disease

J Le Douce, M Maugard, J Veran, M Matos, P Jégo… - Cell metabolism, 2020 - cell.com
Alteration of brain aerobic glycolysis is often observed early in the course of Alzheimer's
disease (AD). Whether and how such metabolic dysregulation contributes to both synaptic …

Scaling up cell-counting efforts in neuroscience through semi-automated methods

IE Bjerke, SC Yates, H Carey, JG Bjaalie, TB Leergaard - Iscience, 2023 - cell.com
Quantifying how the cellular composition of brain regions vary across development, aging,
sex, and disease, is crucial in experimental neuroscience, and the accuracy of different …

Waxholm Space atlas of the rat brain: A 3D atlas supporting data analysis and integration

H Kleven, IE Bjerke, F Clascá, HJ Groenewegen… - Nature …, 2023 - nature.com
Volumetric brain atlases are increasingly used to integrate and analyze diverse
experimental neuroscience data acquired from animal models, but until recently a publicly …

Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool

MA Puchades, G Csucs, D Ledergerber, TB Leergaard… - PloS one, 2019 - journals.plos.org
Modern high throughput brain wide profiling techniques for cells and their morphology,
connectivity, and other properties, make the use of reference atlases with 3D coordinate …

A tool for analyzing electrode tracks from slice histology

P Shamash, M Carandini, K Harris, N Steinmetz - BioRxiv, 2018 - biorxiv.org
It is now possible to record from hundreds of neurons across multiple brain regions in a
single electrophysiology experiment. An essential step in the ensuing data analysis is to …

QUINT: workflow for quantification and spatial analysis of features in histological images from rodent brain

SC Yates, NE Groeneboom, C Coello… - Frontiers in …, 2019 - frontiersin.org
Transgenic animal models are invaluable research tools for elucidating the pathways and
mechanisms involved in the development of neurodegenerative diseases. Mechanistic clues …

Nutil: a pre-and post-processing toolbox for histological rodent brain section images

NE Groeneboom, SC Yates, MA Puchades… - Frontiers in …, 2020 - frontiersin.org
With recent technological advances in microscopy and image acquisition of tissue sections,
further developments of tools are required for viewing, transforming, and analyzing the ever …

AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures

H Kleven, TH Gillespie, L Zehl, T Dickscheid… - Scientific Data, 2023 - nature.com
Brain atlases are important reference resources for accurate anatomical description of
neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for …

A multimodal computational pipeline for 3D histology of the human brain

M Mancini, A Casamitjana, L Peter, E Robinson… - Scientific reports, 2020 - nature.com
Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible
in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic …