The consortium generated high value data for the neuroscience community from mouse, non-human primate and human species over five+ years. The data dashboard allows user to explore how much and what types of data were generated by the BICCN consortium scientists from 2018Q3-2023Q1.
The Data Catalog was updated with new data submitted by BICCN members through end of 2023 Q1. Search the Data Catalog here.
The first release of Allen Brain Cell (ABC) Atlas [BETA] representing ~5,200 newly transcriptomic-defined cell types and their spatial locations across the whole mouse brain is live. This project uses data developed under BICCN and is integrated into the Data Catalog. Read about the new product or access the visualization for these data here.
This data release includes data submitted by BICCN members through end of 2022 Q3. In this release we also added data citation language for ~20 projects and updated specimen counts and other minor changes. Search the Data Catalog here.
One new project was added in this release:
This data release includes data submitted by BICCN members through end of 2022 Q2. In this release we included 5 new BICCN projects:
We also added searchable Specimen metadata with metadata and file manifest downloads for the following projects:
This data release includes information about BICCN data generated through Q1 2022. In this release we added 8 new BICCN projects:
This data release includes information about BICCN data generated through Q3 2021 and includes data from >2800 brains and 37 million cells from 20 different species of mammals. An additional 18 data collections were added. We have now added a “Browse Specimens” button for 2 BICCN projects that allows for search and filter of specimens based on their metadata. We will continue to add this feature to additional projects over time.
Project Summary pages were created for 6 new projects.
This data release includes updates to the BICCN data inventory deposited to data archives through Q2 2021 including more than 2,200 brains (and spinal cords) of imaging data, and >30 million cells of transcriptomic, epigenomic, electrophysiology and morphology data. New data was reported for for 12 new species, adding coverage of a variety of mammals beyond the original human, mouse, and marmoset.
Project Summary pages were created for 14 new projects. Note that data archive URLs will be added as they become available.
This data release documents updates to the inventory of BICCN data deposited at data archives through Q1 2021, including more than 2100 brains of imaging data, and over 25 million single cells of transcriptomic, spatial transcriptomic, epigenomic and morphology data.
New projects and data collections were added this quarter:
This data release contains BICCN data deposited at data archives through Q3 2020, for a total of 1794 brains and over 15 million single cells.
Changes and updates for data access:
The Brain Cell Data Center provides access to the inventory of data generated by the BICCN consortium members. Our initial inventory report, the Cell Registry, is being replaced by a more user-friendly and extensible "Data Inventory". Now you can access information about the data-generating projects of the consortium and their respective data collections. There are many datasets from diverse experimental techniques, and more data is added regularly. New features allow you to search by experimental technique and species, which will make it easier for our community to find datasets of interest. You can access this feature through the Data Access tab.
The eighth BICCN data release contains data from 42 data sets generated by 15 grants. This quarter, 8 new datasets were submitted representing new modalities or new grants.
The seventh BICCN data release included the addition of five new datasets to the BICCN Cell Registry:
New data was also added to existing datasets for an additional 132 brains, 128 sections and 1.1 million cells and nuclei, for a total count of BICCN data of 1,471 brains, 128 sections (spatial transcriptomics) and 11.2 million cells and nuclei.
Changes and updates for data access:
The sixth BICCN data release included the addition of seven new datasets to the BICCN Cell Registry:
New data was also added to existing datasets for an additional 206 brains, and 1.6 million cells and nuclei.
This release brought the total count of BICCN data released to 1,339 brains and 10.1 million cells and nuclei.
The Transcriptomics Explorer enables researchers to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in a web browser. The datasets currently made available for visualization and analysis include data generated under the U19 Zeng and U01 Lein BICCN grants.
New features are released regularly. Currently, researchers can:
The mouse dataset encompasses 75,000 single cells from multiple cortical areas and the hippocampus, providing the basis for comparative studies of cellular diversity in development, evolution, and diseases. This dataset includes SMART-seq v4 transcriptomics data generated under the U19 Zeng grant.
The human dataset encompasses 49,000 nuclei from multiple cortical areas, providing the basis for investigating the cellular diversity across human cortex and directly comparison of cell types with matched regions in mouse. This dataset includes SMART-seq v4 transcriptomics data generated under the U01 Lein grant.
Two new datasets were added to the BICCN Cell Registry, including:
Additionally, new data was added to existing datasets for an additional 196 brains, and 2.2 million cells and nuclei. Altogether, this release brought the total count of BICCN data released to 1,133 brains and 8.5 million cells and nuclei.
The fourth BICCN data release included the addition of five new datasets to the BICCN Cell Registry:
Additionally, new data was added to existing datasets for an additional 103 brains, and 2.4 million cells and nuclei. Altogether, this release brought the total count of BICCN data released since August 2018 to 939 brains and 6.3 million cells and nuclei.
The third BICCN data release included the launch of the Cell Registry. The Cell Registry features data indexing to enable data search and exploration. Users can filter available datasets by technique, species, investigator, grant, specimen type, or modality. The Cell Registry release represents a major infrastructural advancement from prior data access capabilities on the BICCN Portal, as all metadata is now served via API to access data from the Allen Institute for Brain Science Integrated Data Framework.
In addition to updates to existing BICCN datasets, the Cell Registry release included new Project Summary pages, which provide a deeper experimental context for the data in the Cell Registry. Project Summary pages allow enhanced metadata search, such as by anatomic region.
Six Project Summary pages on transcriptomics and epigenomics projects were included in this release:
The second BICCN data release via the BICCN Portal was in December 2018 and included an update to the counts of data deposited by the U01 and U19 data production grantees. This data represented a total of 544 brains, 2,644,600 cells and 8 distinct brain regions profiled by various methods.
The launch of the BICCN Portal in August 2018 supported the first public release of BICCN data. Primary data is available from the Brain Image Library (BIL) at the Pittsburgh Supercomputing Center and the Neuroscience Multi-Omic Archive (NeMO) at University of Maryland. The initial data release of the BICCN was served by a manually curated data access page, with linkages to the BIL and NeMO data archives for primary data access.
Altogether, 20 datasets were released with the launch of the BICCN Portal. These datasets were collected from human, non-human primate, and mouse, and encompassed multiple data modalities including transcriptomics, epigenomics, connectivity, cell morphology, and population imaging.