Cell Type Knowledge Explorer

Posted on February 13th, 2024

The Cell Type Knowledge Explorer (CTKE) is a publicly accessible web application to browse data associated with the multimodal cell census and atlas of primary motor cortex, developed in close collaboration with the BRAIN Initiative Cell Census Network (BICCN). The CTKE includes access to single-cell transcriptomic and epigenomic profiling of human, marmoset, and mouse primary motor cortex, with additional data sets assessing the spatial distribution, cell morphology (shape), and electrical properties of these cell types. All data powering the CTKE is provided to encourage cell exploration by scientists, students, and educators through the browser and linked resources.

Allen Brain Cell (ABC) Atlas

Posted on February 13th, 2024

The Allen Brain Cell (ABC) Atlas provides a platform for visualizing and analyzing multimodal single cell and spatial transcriptomics data across the whole mammalian brain in multiple datasets simultaneously. This open science resource, developed by the Allen Institute as part of the Brain Knowledge Platform, allows unprecedented insights into the enormous diversity of cell types in the brain and where they are. The ABC Atlas will enable the neuroscience community to identify more cell types in the brain, investigate the spatial location of cell types, investigate gene expression and co-expression patterns in cell types, and refine boundaries and knowledge of brain regions defined by gene expression. The Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas opening up endless possibilities for discoveries and breakthroughs in neuroscience.

MapMyCells

Posted on February 13th, 2024

MapMyCells is a web tool that allows scientists worldwide to assign cell types to their own transcriptomics and spatial data by comparing their data to massive mammalian brain reference taxonomies derived by the Allen Institute for Brain Science and the BRAIN Initiative Cell Atlas Network (BICAN). Researchers follow a simple process to map their gene expression: (1) upload a cell by gene matrix, (2) choose from available reference taxonomies and mapping algorithms, (3) download the reference cell type assignments for their data when the mapping is complete. Methods and data used in this tool will be publicly accessible for code-based applications as well.

Pinpoint

Posted on March 1st, 2023

Pinpoint is a trajectory planning tool for acute and chronic electrophysiology recordings as well as injections. Using an interactive 3D scene, Pinpoint allows researchers to plan multi-probe insertions in an intuitive environment, all in the convenience of your web browser. Users can explore different options for craniotomies and check that insertions will not interfere with other parts of a surgical implant or recording rig. During live experiments, Pinpoint can be linked to hardware micro-manipulators as well as data acquisition software, allowing you to follow along as your probes are placed into position inside the brain, and forward that anatomical information to be viewed alongside your live data.

NEMAR.org

Posted on August 19th, 2022

The Neuroelectromagnetic Data Archive and Tools Resource (NEMAR) is a gateway to OpenNeuro for research using publicly available human NEM data (EEG, MEG, iEEG/ECoG). NEM data made available on OpenNeuro can be analyzed in place via the Neuroscience Gateway (NSG, nsgportal.org). We are building web applications to evaluate the quality of uploaded NEM data, to visualize the data, and an easy-to-use pathway to apply user-specified processing to the data via NSG, without requiring data download and re-upload.

BossDB – Brain Observatory Storage Service and Database

Posted on August 19th, 2022

BossDB (Brain Observatory Storage Service and Database, https://bossdb.org) is a cloud-based data ecosystem for large-scale volumetric 3D and 4D neuroimaging data. BossDB focuses primarily on storing volumetric Electron Microscopy (EM) and X-Ray Microtomography (XRM) datasets generated as a part of the BRAIN Initiative. BossDB stores high resolution, multi-channel image data with registered segmentations, annotations, and meshes, and connects to a number of community resources for data access and data visualization. BossDB also stores connectomics datasets and contains a number of software tools and interfaces for querying and searching connectomes.

Data Archive for the BRAIN Initiative (DABI)

Posted on August 19th, 2022

DABI is a web-accessible data archive that captures, stores, and curates human invasive neurophysiology data from BRAIN Initiative proposals. These data are aggregated, organized, and disseminated to the research community to accelerate the pace of discovery in the neurosciences. In addition to its archival and organization services, DABI also integrates novel analytical tools for cohort discovery and preliminary analyses.

DANDI

Posted on August 19th, 2022

DANDI is the BRAIN Initiative supported data archive for publishing and sharing
neurophysiology data including electrophysiology, optophysiology, and
behavioral time-series, and images from immunostaining experiments. The archive
supports a broad range of users with different levels of expertise by providing
a spectrum from web-based to programmatic mechanisms to access and upload data
and helps improve the expertise through training of the scientific user base
through tutorials and workshops. All aspects of DANDI infrastructure are
developed with an adherence to open software, explicit licensing, and community
standards.

OpenNeuro

Posted on August 19th, 2022

OpenNeuro is a data archive that provides the ability to openly share data from a broad range of brain imaging data types following the FAIR principles for data sharing. Uploaded datasets are made available with minimal restrictions to the public at large, in order to permit maximal reuse. OpenNeuro accepts datasets formatted according to the Brain Imaging Data Structure (BIDS) standard, a community-developed standard that aims to achieve broad coverage of neuroimaging data types while unifying metadata.

PET2BIDS

Posted on August 19th, 2022

This repository hosts tools to curate PET brain data using the Brain Imaging Data Structure Specification. The work to create these tools is funded by Novo Nordisk Fonden (NNF20OC0063277) and the BRAIN initiative (MH002977-01). This tool extracts and outputs some of the additional blood and radiological data along with PET neuroimaging data into the Brain Imaging Data Structure. It is one of the few tools that exists to aid in this conversion and is being used to convert and share data on OpenNeuro.org.