Jan Gunnar Bjaalie

Siibra: A software tool suite for realizing a Multilevel Human Brain Atlas from complex data resources

The paper introduces siibra, a software tool suite that integrates diverse brain data into a Multilevel Human Brain Atlas, enabling interoperable analysis and visualization.

An interactive 3D atlas of gene expression in the mouse brain

The paper improves the resolution of the Allen Mouse Brain Atlas to 25 micrometers cubed for 4,083 genes and provides an interactive platform for exploring gene expression patterns.

Software and pipelines for registration and analyses of rodent brain image data in reference atlas space

The paper presents software tools for registering and analyzing rodent brain image data in reference atlas space, enabling spatially informed analysis of anatomical and molecular features.

DeMBA: a developmental atlas for navigating the mouse brain in space and time

DeMBA provides a 4D atlas of the developing mouse brain from postnatal day 4 to 56, enabling spatial and temporal analysis with software tools for registration and coordinate transformation.

An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain

The paper extends and improves the CCFv3 atlas to cover missing brain regions and enhance alignment for better cell type mapping and data integration.

The developing mouse dopaminergic system: Cortical-subcortical shift in D1/D2 receptor balance and increasing regional differentiation

This study quantifies D1 and D2 receptor cell densities in mouse forebrain across development, revealing a cortico-subcortical shift and sex differences in maturational patterns.

Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model

The paper analyzes genetic diversity's effect on brain composition in an Alzheimer's disease mouse model using an enhanced QUINT workflow.

DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas

DeepSlice automatically registers mouse brain histology to the Allen Brain Atlas, achieving high accuracy and speed improvements of over 1000 times.

AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures

The paper introduces AtOM, an ontology model to standardize brain atlas representation, enabling interoperability and data integration across species and atlas versions.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

Topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1

The paper shows that Nr2f1 gene expression in postmitotic neurons controls corticopontine topographic mapping, while its expression in progenitor cells affects the ratio of corticopontine to corticospinal fibers.

3D atlas of the pituitary gland of the model fish medaka

This paper creates the first 3D atlas of the medaka pituitary, revealing spatial distributions of endocrine cell types and sexual dimorphism in gene expression.