Connectomics & Brain Mapping
Whole-brain connectomes, cubic-millimeter cortical reconstructions, expansion microscopy and brain-wide cell atlases.
Most influential
- An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging
In this paper we describe a method for retrospective estimation and correction of eddy current (EC)-induced distortions and subject movement in diffusion imaging. In addition a susceptibility-induced field can be supplied and will be incorporated into the calculations in a way that accurately reflects that the two fields (susceptibility- and EC-induced) beha…
Abstract excerpt by Andersson JLR et al., CC-BY, https://doi.org/10.1016/j.neuroimage.2015.10.019; truncated.
Article3,382 citationsdoi:10.1016/j.neuroimage.2015.10.019 - BrainNet Viewer: a network visualization tool for human brain connectomics
The human brain is a complex system whose topological organization can be represented using connectomics. Recent studies have shown that human connectomes can be constructed using various neuroimaging technologies and further characterized using sophisticated analytic strategies, such as graph theory. These methods reveal the intriguing topological architect…
Abstract excerpt by Xia M et al., CC-BY, https://doi.org/10.1371/journal.pone.0068910; truncated.
Article3,349 citationsdoi:10.1371/journal.pone.0068910 - A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of app…
Abstract excerpt by Zizhen Yao et al., CC-BY, https://doi.org/10.1038/s41586-023-06812-z; truncated.
Article1,325 citationsdoi:10.1038/s41586-023-06812-z - Neuronal wiring diagram of an adult brain
Abstract Connections between neurons can be mapped by acquiring and analysing electron microscopic brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative 1–6 , but nevertheless inadequate for understanding brain function more globally. Here we present a neuronal wir…
Abstract excerpt by Sven Dorkenwald et al., CC-BY, https://doi.org/10.1038/s41586-024-07558-y; truncated.
Article574 citationsdoi:10.1038/s41586-024-07558-y - Whole-brain annotation and multi-connectome cell typing of Drosophila
Abstract The fruit fly Drosophila melanogaster has emerged as a key model organism in neuroscience, in large part due to the concentration of collaboratively generated molecular, genetic and digital resources available for it. Here we complement the approximately 140,000 neuron FlyWire whole-brain connectome 1 with a systematic and hierarchical annotation of…
Abstract excerpt by Philipp Schlegel et al., CC-BY, https://doi.org/10.1038/s41586-024-07686-5; truncated.
Article412 citationsdoi:10.1038/s41586-024-07686-5 - The challenge of mapping the human connectome based on diffusion tractography
Tractography based on non-invasive diffusion imaging is central to the study of human brain connectivity. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain data set with ground truth tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions …
Abstract excerpt by Maier-Hein KH et al., CC-BY, https://doi.org/10.1038/s41467-017-01285-x; truncated.
Article1,123 citationsdoi:10.1038/s41467-017-01285-x - A connectome and analysis of the adult <i>Drosophila</i> central brain
The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster . Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine…
Abstract excerpt by Scheffer LK et al., CC-BY, https://doi.org/10.7554/elife.57443; truncated.
Review968 citationsdoi:10.7554/elife.57443 - Deterministic diffusion fiber tracking improved by quantitative anisotropy
Diffusion MRI tractography has emerged as a useful and popular tool for mapping connections between brain regions. In this study, we examined the performance of quantitative anisotropy (QA) in facilitating deterministic fiber tracking. Two phantom studies were conducted. The first phantom study examined the susceptibility of fractional anisotropy (FA), gener…
Abstract excerpt by Yeh FC et al., CC-BY, https://doi.org/10.1371/journal.pone.0080713; truncated.
Article962 citationsdoi:10.1371/journal.pone.0080713 - The hubs of the human connectome are generally implicated in the anatomy of brain disorders
Brain networks or 'connectomes' include a minority of highly connected hub nodes that are functionally valuable, because their topological centrality supports integrative processing and adaptive behaviours. Recent studies also suggest that hubs have higher metabolic demands and longer-distance connections than other brain regions, and therefore could be cons…
Abstract excerpt by Crossley NA et al., CC-BY, https://doi.org/10.1093/brain/awu132; truncated.
Article959 citationsdoi:10.1093/brain/awu132 - GRETNA: a graph theoretical network analysis toolbox for imaging connectomics
Recent studies have suggested that the brain's structural and functional networks (i.e., connectomics) can be constructed by various imaging technologies (e.g., EEG/MEG; structural, diffusion and functional MRI) and further characterized by graph theory. Given the huge complexity of network construction, analysis and statistics, toolboxes incorporating these…
Abstract excerpt by Wang J et al., CC-BY, https://doi.org/10.3389/fnhum.2015.00386; truncated.
Article958 citationsdoi:10.3389/fnhum.2015.00386 - Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster
High-resolution electron microscopy of nervous systems has enabled the reconstruction of synaptic connectomes. However, we do not know the synaptic sign for each connection (i.e., whether a connection is excitatory or inhibitory), which is implied by the released transmitter. We demonstrate that artificial neural networks can predict transmitter types for pr…
Abstract excerpt by Nils Eckstein et al., CC-BY, https://doi.org/10.1016/j.cell.2024.03.016; truncated.
Article214 citationsdoi:10.1016/j.cell.2024.03.016 - Sex Differences in the Adult Human Brain: Evidence from 5216 UK Biobank Participants
Sex differences in the human brain are of interest for many reasons: for example, there are sex differences in the observed prevalence of psychiatric disorders and in some psychological traits that brain differences might help to explain. We report the largest single-sample study of structural and functional sex differences in the human brain (2750 female, 2…
Abstract excerpt by Ritchie SJ et al., CC-BY, https://doi.org/10.1093/cercor/bhy109; truncated.
Article649 citationsdoi:10.1093/cercor/bhy109 - FlyWire: online community for whole-brain connectomicsArticle289 citationsdoi:10.1038/s41592-021-01330-0
- BrainSpace: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets
Understanding how cognitive functions emerge from brain structure depends on quantifying how discrete regions are integrated within the broader cortical landscape. Recent work established that macroscale brain organization and function can be described in a compact manner with multivariate machine learning approaches that identify manifolds often described a…
Abstract excerpt by Vos de Wael R et al., CC-BY, https://doi.org/10.1038/s42003-020-0794-7; truncated.
Article580 citationsdoi:10.1038/s42003-020-0794-7 - TractSeg - Fast and accurate white matter tract segmentation
The individual course of white matter fiber tracts is an important factor for analysis of white matter characteristics in healthy and diseased brains. Diffusion-weighted MRI tractography in combination with region-based or clustering-based selection of streamlines is a unique combination of tools which enables the in-vivo delineation and analysis of anatomic…
Abstract excerpt by Wasserthal J et al., CC-BY, https://doi.org/10.1016/j.neuroimage.2018.07.070; truncated.
Article582 citationsdoi:10.1016/j.neuroimage.2018.07.070
Newest work
- Every route counts, but some count more: a max-plus view of the C. elegans brainPreprintarXiv:2610.37587
- Which build of the connectome a whole-brain fly model runs on changes what it can doArticledoi:10.5281/zenodo.23678525
- Phase response approach to networked neural activity models with delaysPreprintarXiv:2610.35638
- Flybrain: an untrained, connectome-faithful simulation of the whole Drosophila brain and nerve cord, and what its memory system suggests for continual learning in AIArticledoi:10.5281/zenodo.23648099
- Sensorimotor behaviour from an untrained brain-and-nerve-cord connectomePreprintarXiv:2610.33881
- Cross-species molecular mapping of the photoreceptor sensory cilium and periciliary structures identifies conserved and species-specific architectural featuresArticledoi:10.1242/jcs.265080
- Multivariate prediction of white matter BOLD activity and its relationship to marginal connectivityArticledoi:10.1016/j.neuroimage.2026.122297
- Longitudinal fMRI reveals multi-network reconfiguration and a recurrent frontoparietal shift across rest and task states during adult agingPreprintarXiv:2610.24433
- Reciprocity coordinates a three-way trade-off in recurrent neural circuitsPreprintarXiv:2610.19949
- Years-long stability of X10 expansion microscopy hydrogelsArticledoi:10.1186/s13036-026-00781-3