BrainCircuits.io Web Application
Comparative circuit analyses
Datasets from different species or different developmental stages or brain regions can be displayed alongside each other
Widgets belong to a specific dataset, thereby allowing the creation of very flexible layouts and workflows across datasets for analysis, annotation and visualization
Large-scale dataset support
Supporting datasets with billions of supervoxels, and hundreds of millions of synaptic links or vesicles for querying, aggregation and visualization
Subsecond latency for querying large datasets and graphs
Visualization provided by Neuroglancer from Google
Multi-modal multi-scale data model
Data model supports representation at different scales
Representation of regions, neurons, synapses, skeletons, mitochondria, vesicles (point annotations)
Arbitrary properties can be associated with basic types, such as neurotransmitter data or other measured data
Permission control
Collaborative community proofreading datasets with special protected permission control to manage pre-publication access
Integration with the CAVE framework to reuse access permissions of datasets with ongoing community proofreading
Adherence to community guidelines for rules and recommendations
Pre-publication datasets can be configured as private for dedicated access
Brain region nomenclature
Central nervous system regions of interest are organized with existing nomenclatures or ontologies, providing identifiers
Cross-link brain and ventral nerve cord regions in fruit flies with Virtual Fly Brain
Regions are linked with their corresponding mesh identifiers if available for a specific dataset
Annotation support
Annotation data about segments can be retrieved from different sources and displayed in the data tables
Supported sources are for instance existing CAVE tables, or shared spreadsheets
Proofreading integration with CAVE
Provides up-to-date materialization of current state of proofreading a dataset
Summary statistics about segments are generated in regular intervals to keep information up-to-date to guide proofreading
Access and browse all CAVE tables in a project and its content
Customizable layouts for workspaces
The layout of the web application can be arranged flexibly based on the required workflow, such as when comparing neurons and circuits across different datasets
Matching neurons with genetic lines collections
Reconstructed neurons can be transformed to template spaces and ranked against existing genetic lines collection to discover existing lines for follow-up functional and behavioral experiments
Cross-linking genetic lines to existing databases, such as Janelia NeuronBridge for fruit flies
Matching neurons with EM datasets
Using the ColorMIP matching approach EM neurons can be matched to other EM neurons in the same and different datasets. Useful for finding homologous cell types in other datasets, or the same cell type on the contralateral side
Programmatic access via API
Datasets can be accessed via REST API protected by token-based authentication
Resources page
A growing list of tools and resources that are useful for connectomics research
Covering tools and resources for all aspects of the data processing pipeline from data acquisition, alignment & registration, segmentation & proofreading, exploration & analysis
BrainCircuits.io Widgets
About Widget
A short description about the dataset including information about data size, resolutions etc.
A list of associated weblinks and publication about the dataset
Queries Widget
Simple interface to run predefined queries against the dataset
Find relevant queries by filtering
Request additional queries based on you needs
Segments Widget
Search for segments in the dataset based on segment ID or annotation label
Display any number of per segment properties (like size, labels, etc.) which may differ based on the data available for the dataset
Download CSV of segments table
Filter segments by any combination of values for each column
Choose color of subsets of segments and show them in Neuroglancer
Open other widgets directly, such as Connectivity or Graphic Walker widget for analysis
Connectivity Widget
Show upstream and downstream segments with synaptic counts for a set of source segments
Filtering and display options like in the Segments widget for all segments
Color and display up- downstream segments in Neuroglancer
Neuron Network Widget
Display network diagram for segment connectivity
Choose layouting algorithm
Filter network by synaptic count thresholds
Show annotations per node
Segments Info Widget
Display segment specific properties, such as annotations etc.
Regions Widget
List of species-specific nervous system regions, tracts, etc
Based on common anatomy nomenclature for the fruitly (Ito et al. 2014, Court et al. 2017)
Matching of regions in fruitfly to Virtual Fly Brain
Full-text search of regions
Available region meshes can be toggled in the Neuroglancer widget
Relevant paragraphs from scientific publications with information about region
ChangeLog Widget
Display proofreading edit information for a set of segments from the CAVE framework
List of individual edits and aggregate edits by user/affiliation/lab
Combine Widgets
Arbitray widgets from any available datasets can be selected and added to the current workspace
This allows for creation of customized layouts for comparative connectomic analyses
Graphic Walker Widget
An open-source alternative to the widely used Tableau framework
Segments and their properties can be loaded directly into the widget
Allows user friendly drag and drop based generation of visualizations for exploratory analyses
Allow very flexible modification of visualizations, their properties, and export functionality
Genetic Lines Widget
Retrieve ColorMIPs for published genetic lines by searching by line name
ColorMIPs Widget
Retrieve precomputed colorMIPs or generate colorMIPs on-the-fly for CAVE-backed community datasets
Select ColorMIPs as search image to quickly query against other ColorMIPs in over 100 collections (EM+LM+Aggregate collections) totalling over 830k ColorMIP images
Neuroglancer Widget
Neuroglancer used for large-scale 3D visualization
Changing of background color
Copy-paste visible segmentIDs for further processing in other widgets
Proofreading Widget
Uses the Neuroglancer-based proofreading interface from the CAVE framework
New widgets can be developed from scratch with minimial effort using the React framework and by accessing datasets via standardized BrainCircuits.io API calls. A new widget is useful for all datasets on the platform if the required data is available.
Please get in contact if you have a request for a new widget or enhancement for existing widgets.
Please get in contact if you have a request for a new widget or enhancement for existing widgets.