CAVE: Connectome Annotation Versioning Engine DOI Creative Commons
Sven Dorkenwald, Casey M Schneider-Mizell, Derrick Brittain

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июль 28, 2023

Abstract Advances in Electron Microscopy, image segmentation and computational infrastructure have given rise to large-scale richly annotated connectomic datasets which are increasingly shared across communities. To enable collaboration, users need be able concurrently create new annotations correct errors the automated by proofreading. In large datasets, every proofreading edit relabels cell identities of millions voxels thousands like synapses. For analysis, require immediate reproducible access this constantly changing expanding data landscape. Here, we present Connectome Annotation Versioning Engine (CAVE), a for connectome analysis up-to petascale (∼1mm 3 ) while annotating is ongoing. segmentation, CAVE provides distributed continuous versioning reconstructions. Annotations defined locations such that they can quickly assigned underlying segment enables fast queries CAVE’s arbitrary time points. supports schematized, extensible annotations, so researchers readily design novel annotation types. already used many connectomics including largest available date.

Язык: Английский

Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster DOI Creative Commons
Nils Eckstein, Alexander Shakeel Bates, Andrew Champion

и другие.

Cell, Год журнала: 2024, Номер 187(10), С. 2574 - 2594.e23

Опубликована: Май 1, 2024

High-resolution electron microscopy of nervous systems has enabled the reconstruction synaptic connectomes. However, we do not know sign for each connection (i.e., whether a is excitatory or inhibitory), which implied by released transmitter. We demonstrate that artificial neural networks can predict transmitter types presynapses from micrographs: network trained to six transmitters (acetylcholine, glutamate, GABA, serotonin, dopamine, octopamine) achieves an accuracy 87% individual synapses, 94% neurons, and 91% known cell across D. melanogaster whole brain. visualize ultrastructural features used prediction, discovering subtle but significant differences between phenotypes. also analyze distributions brain find neurons develop together largely express only one fast-acting GABA). hope our publicly available predictions act as accelerant neuroscientific hypothesis generation fly.

Язык: Английский

Процитировано

114
Whole-brain annotation and multi-connectome cell typing of Drosophila DOI Creative Commons
Philipp Schlegel, Yijie Yin, Alexander Shakeel Bates

и другие.

Nature, Год журнала: 2024, Номер 634(8032), С. 139 - 152

Опубликована: Окт. 2, 2024

Язык: Английский

Процитировано

84
Connectome-driven neural inventory of a complete visual system DOI Creative Commons
Aljoscha Nern, Frank Loesche, Shin-ya Takemura

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 18, 2024

Vision provides animals with detailed information about their surroundings, conveying diverse features such as color, form, and movement across the visual scene. Computing these parallel spatial requires a large network of neurons, that in distant flies humans, regions comprise half brain's volume. These brain often reveal remarkable structure-function relationships, neurons organized along maps shapes directly relate to roles processing. To unravel stunning diversity complex system, careful mapping neural architecture matched tools for targeted exploration circuitry is essential. Here, we report new connectome right optic lobe from male Drosophila central nervous system FIB-SEM volume comprehensive inventory fly's neurons. We developed computational framework quantify anatomy establishing basis interpreting how vision. By integrating this analysis connectivity information, neurotransmitter identity, expert curation, classified ~53,000 into 727 types, which are systematically described named first time. Finally, share an extensive collection split-GAL4 lines our neuron type catalog. Together, set data unlock possibilities systematic investigations vision Drosophila, foundation deeper understanding sensory

Язык: Английский

Процитировано

27
Network statistics of the whole-brain connectome of Drosophila DOI Creative Commons
Albert Lin, Runzhe Yang, Sven Dorkenwald

и другие.

Nature, Год журнала: 2024, Номер 634(8032), С. 153 - 165

Опубликована: Окт. 2, 2024

Язык: Английский

Процитировано

26
Neuronal parts list and wiring diagram for a visual system DOI Creative Commons
Arie Matsliah, Szi-chieh Yu, Krzysztof Kruk

и другие.

Nature, Год журнала: 2024, Номер 634(8032), С. 166 - 180

Опубликована: Окт. 2, 2024

Язык: Английский

Процитировано

23
Nested neural circuits generate distinct acoustic signals during Drosophila courtship DOI Creative Commons
Joshua L. Lillvis, Kaiyu Wang, Hiroshi Shiozaki

и другие.

Current Biology, Год журнала: 2024, Номер 34(4), С. 808 - 824.e6

Опубликована: Янв. 30, 2024

Many motor control systems generate multiple movements using a common set of muscles. How are premotor circuits able to flexibly diverse movement patterns? Here, we characterize the neuronal that drive distinct courtship songs Drosophila melanogaster. Male flies vibrate their wings toward females produce two different song modes—pulse and sine song—which signal species identity male quality. Using cell-type-specific genetic reagents connectome, provide cellular synaptic map in ventral nerve cord these examine how activating or inhibiting each cell type within affects song. Our data reveal circuit is organized into nested feedforward pathways with extensive reciprocal feedback connections. The larger network produces pulse song, more complex ancestral form. A subset this simpler recent Such organization may be feature which evolution has layered increasing flexibility onto basic pattern.

Язык: Английский

Процитировано

21
A Drosophila computational brain model reveals sensorimotor processing DOI Creative Commons
Philip K. Shiu, Gabriella R Sterne, Nico Spiller

и другие.

Nature, Год журнала: 2024, Номер 634(8032), С. 210 - 219

Опубликована: Окт. 2, 2024

Язык: Английский

Процитировано

19
Functional connectomics spanning multiple areas of mouse visual cortex DOI Creative Commons
J. Alexander Bae,

Mahaly Baptiste,

Maya R. Baptiste

и другие.

Nature, Год журнала: 2025, Номер 640(8058), С. 435 - 447

Опубликована: Апрель 9, 2025

Abstract Understanding the brain requires understanding neurons’ functional responses to circuit architecture shaping them. Here we introduce MICrONS connectomics dataset with dense calcium imaging of around 75,000 neurons in primary visual cortex (VISp) and higher areas (VISrl, VISal VISlm) an awake mouse that is viewing natural synthetic stimuli. These data are co-registered electron microscopy reconstruction containing more than 200,000 cells 0.5 billion synapses. Proofreading a subset yielded reconstructions include complete dendritic trees as well local inter-areal axonal projections map up thousands cell-to-cell connections per neuron. Released open-access resource, this includes tools for retrieval analysis 1,2 . Accompanying studies describe its use comprehensive characterization cell types 3–6 , synaptic level connectivity diagram cortical column 4 uncovering cell-type-specific inhibitory can be linked gene expression 4,7 Functionally, identify new computational principles how information integrated across space 8 characterize novel neuronal invariances 9 bring structure function together uncover general principle between excitatory within 10,11

Язык: Английский

Процитировано

7
Perisomatic ultrastructure efficiently classifies cells in mouse cortex DOI Creative Commons
Leila Elabbady, Sharmishtaa Seshamani, Shang Mu

и другие.

Nature, Год журнала: 2025, Номер 640(8058), С. 478 - 486

Опубликована: Апрель 9, 2025

Abstract Mammalian neocortex contains a highly diverse set of cell types. These types have been mapped systematically using variety molecular, electrophysiological and morphological approaches 1–4 . Each modality offers new perspectives on the variation biological processes underlying cell-type specialization. Cellular-scale electron microscopy provides dense ultrastructural examination an unbiased perspective subcellular organization brain cells, including their synaptic connectivity nanometre-scale morphology. In data that contain tens thousands neurons, most which incomplete reconstructions, identifying becomes clear challenge for analysis 5 Here, to address this challenge, we present systematic survey somatic region all cells in cubic millimetre cortex quantitative features obtained from microscopy. This demonstrates perisomatic is sufficient identify types, defined primarily basis patterns. We then describe how classification facilitates cell-type-specific characterization locating with rare patterns dataset.

Язык: Английский

Процитировано

6
Connectome-driven neural inventory of a complete visual system DOI Creative Commons
Aljoscha Nern, Frank Loesche, Shin-ya Takemura

и другие.

Nature, Год журнала: 2025, Номер unknown

Опубликована: Март 26, 2025

Abstract Vision provides animals with detailed information about their surroundings and conveys diverse features such as colour, form movement across the visual scene. Computing these parallel spatial requires a large network of neurons. Consequently, from flies to humans, regions in brain constitute half its volume. These often have marked structure–function relationships, neurons organized along maps shapes that directly relate roles processing. More than century anatomical studies catalogued detail cell types fly systems 1–3 , behavioural physiological experiments examined capabilities flies. To unravel diversity complex system, careful mapping neural architecture matched tools for targeted exploration this circuitry is essential. Here we present connectome right optic lobe male Drosophila melanogaster acquired using focused ion beam milling scanning electron microscopy. We established comprehensive inventory developed computational framework quantify anatomy. Together, data establish basis interpreting how vision. By integrating analysis connectivity information, neurotransmitter identity expert curation, classified approximately 53,000 into 732 types. are systematically described newly named. Finally, share an extensive collection split-GAL4 lines our neuron-type catalogue. Overall, set unlocks new possibilities systematic investigations vision foundation deeper understanding sensory

Язык: Английский

Процитировано

2