Whole-body integration of gene expression and single-cell morphology

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Whitening of odor representations by the wiring diagram of the olfactory bulb

(2020) Adrian A. Wanner et al.   NATURE NEUROSCIENCE

A genetic, genomic, and computational resource for exploring neural circuit function

(2020) Fred P Davis et al.   eLife

A connectome and analysis of the adult Drosophila central brain

(2020) Louis K Scheffer et al.   eLife

Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

(2020) Ezequiel Miron et al.   Science Advances

Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development

(2019) Kai Zhang et al.   Science Advances

Neuronal cell types in the annelid Platynereis dumerilii

(2019) Elizabeth A Williams et al.   CURRENT OPINION IN NEUROBIOLOGY

Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics

(2019) Alexander Shakeel Bates et al.   CURRENT OPINION IN NEUROBIOLOGY

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

A repeated molecular architecture across thalamic pathways

(2019) James W. Phillips et al.   NATURE NEUROSCIENCE

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

From spiral cleavage to bilateral symmetry: the developmental cell lineage of the annelid brain

(2019) Pavel Vopalensky et al.   BMC BIOLOGY

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

(2019) Dong-Wook Kim et al.   CELL

High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing

(2019) Xiaoyin Chen et al.   CELL

Probabilistic cell typing enables fine mapping of closely related cell types in situ

(2019) Xiaoyan Qian et al.   NATURE METHODS

An ancestral apical brain region contributes to the central complex under the control of foxQ2 in the beetle Tribolium

(2019) Bicheng He et al.   eLife

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

(2018) Arnau Sebé-Pedrós et al.   CELL

Large Scale Image Segmentation with Structured Loss based Deep Learning for Connectome Reconstruction

(2018) Jan Funke et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body

(2018) Kaia Achim et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-precision automated reconstruction of neurons with flood-filling networks

(2018) Michał Januszewski et al.   NATURE METHODS

Functional architecture of reward learning in mushroom body extrinsic neurons of larval Drosophila

(2018) Timo Saumweber et al.   Nature Communications

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy

(2018) Atsushi Matsuda et al.   Scientific Reports

Early metazoan cell type diversity and the evolution of multicellular gene regulation

(2018) Arnau Sebé-Pedrós et al.   Nature Ecology & Evolution

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy

(2018) Benjamin Titze et al.   Frontiers in Neural Circuits

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Whole-head recording of chemosensory activity in the marine annelid Platynereis dumerilii

(2018) Thomas F. Chartier et al.   Open Biology

Neural circuitry of a polycystin-mediated hydrodynamic startle response for predator avoidance

(2018) Luis A Bezares-Calderón et al.   eLife

The importance of identified neurons in gastropod molluscs to neuroscience

(2018) Paul S Katz et al.   CURRENT OPINION IN NEUROBIOLOGY

Cholinergic/glutamatergic co-transmission in striatal cholinergic interneurons: new mechanisms regulating striatal computation

(2017) Ornela Kljakic et al.   JOURNAL OF NEUROCHEMISTRY

Multicut brings automated neurite segmentation closer to human performance

(2017) Thorsten Beier et al.   NATURE METHODS

Strategic and practical guidelines for successful structured illumination microscopy

(2017) Justin Demmerle et al.   Nature Protocols

Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord ofPlatynereis dumerilii

(2017) Hernando Martínez Vergara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

(2017) Ed Lein et al.   SCIENCE

Correlating Anatomy and Function with Gene Expression in Individual Neurons by Combining in Vivo Labeling, Patch Clamp, and Single Cell RNA-seq

(2017) Carsten K. Pfeffer et al.   Frontiers in Cellular Neuroscience

Ciliomotor circuitry underlying whole-body coordination of ciliary activity in the Platynereis larva

(2017) Csaba Verasztó et al.   eLife

Synaptic and peptidergic connectome of a neurosecretory center in the annelid brain

(2017) Elizabeth A Williams et al.   eLife

Volume scanning electron microscopy for imaging biological ultrastructure

(2016) Benjamin Titze et al.   BIOLOGY OF THE CELL

Developmental interneuron subtype deficits after targeted loss of Arx

(2016) Eric D. Marsh et al.   BMC NEUROSCIENCE

Revisiting Neuronal Cell Type Classification in Caenorhabditis elegans

(2016) Oliver Hobert et al.   CURRENT BIOLOGY

Nematode nervous systems

(2016) William Schafer   CURRENT BIOLOGY

Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb

(2016) Adrian A Wanner et al.   NATURE NEUROSCIENCE

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons

(2016) Adrian A. Wanner et al.   Scientific Data

Saturated Reconstruction of a Volume of Neocortex

(2015) Narayanan Kasthuri et al.   CELL

A multilevel multimodal circuit enhances action selection in Drosophila

(2015) Tomoko Ohyama et al.   NATURE

BigDataViewer: visualization and processing for large image data sets

(2015) Tobias Pietzsch et al.   NATURE METHODS

Genealogical correspondence of a forebrain centre implies an executive brain in the protostome–deuterostome bilaterian ancestor

(2015) Gabriella H. Wolff et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy

(2015) Graeme Ball et al.   Scientific Reports

Inter-individual stereotypy of the Platynereis larval visual connectome

(2015) Nadine Randel et al.   eLife

Illuminating the Base of the Annelid Tree Using Transcriptomics

(2014) Anne Weigert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Neuronal connectome of a sensory-motor circuit for visual navigation

(2014) Nadine Randel et al.   eLife

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes

(2013) Daniel J. Bumbarger et al.   CELL

The bilaterian forebrain: an evolutionary chimaera

(2013) Maria Antonietta Tosches et al.   CURRENT OPINION IN NEUROBIOLOGY

ImgLib2—generic image processing in Java

(2012) Tobias Pietzsch et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

TrakEM2 Software for Neural Circuit Reconstruction

(2012) Albert Cardona et al.   PLoS One

A GAL4-Driver Line Resource for Drosophila Neurobiology

(2012) Arnim Jenett et al.   Cell Reports

Whole-body gene expression pattern registration in Platynereis larvae

(2012) Albina Asadulina et al.   EvoDevo

The Virtual Fly Brain browser and query interface

(2011) N. Milyaev et al.   BIOINFORMATICS

Brain Homology: Dohrn of a New Era?

(2011) Nicholas James Strausfeld   BRAIN BEHAVIOR AND EVOLUTION

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

A high-level 3D visualization API for Java and ImageJ

(2010) Benjamin Schmid et al.   BMC BIOINFORMATICS

Profiling by Image Registration Reveals Common Origin of Annelid Mushroom Bodies and Vertebrate Pallium

(2010) Raju Tomer et al.   CELL

Three consecutive generations of nephridia occur during development of Platynereis dumerilii (Annelida, Polychaeta)

(2010) Christian Hasse et al.   DEVELOPMENTAL DYNAMICS

Retinal patterning by Pax6-dependent cell adhesion molecules

(2010) Elisabeth Rungger-Brändle et al.   Developmental Neurobiology

Comparative neuroanatomy suggests repeated reduction of neuroarchitectural complexity in Annelida

(2010) Carsten M Heuer et al.   Frontiers in Zoology

elastix: A Toolbox for Intensity-Based Medical Image Registration

(2009) S. Klein et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Mechanism of phototaxis in marine zooplankton

(2008) Gáspár Jékely et al.   NATURE