NIMP: Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation (RRID:SCR_024684)

NIMP is developed under NIH BRAIN Initiative's BICAN U24MH130988 award as a part of the coordinating unit for biostatistics, informatics, and engagement (CUBIE) for the BRAIN Initiative Cell Atlas Network (BICAN) program.

NIMP consists of two portals for BICAN collaborative data generation: the Specimen Portal and the Sequence Library (SeqLib) Portal. The Specimen Portal focuses on tissue management from donors to brain slabs and annotated brain samples. The SeqLib Portal manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent, data-modality-specific archives. Both portals work in tandem to generate multimodal genomic data that can be traced back to their anatomical origins using the Allen Brain Atlas.

The portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. All of the underlying functionalities are achieved through a robust agile development strategy using NHash resource identifiers, metadata standardization, active combinatorial dashboarding, resource provenance linkage and rendering (e.g. Sankey diagrams), and dedicated interfaces with NIH Neuro Biobank, sequencing centers, NeMO, and the larger BICAN data ecosystem.

Frequently Asked Questions

Please click the “Sign-up” button on the top-right of the landing page to start the sign-up process.

To request a specific user role such as Brain Bank Personnel or Library Submitter, you need to indicate this in the "Message" text box on the sign-up page. If you have already signed up, please email Shiqiang Tao ([email protected]) what user role you need.

Contact the user who is the manager of the Lab in the portal to have you added to the Lab.

The User Guide contain a glossary of terms describing the meanings of the terms used in the portal.

Yes, the portal has an API for data access. More information can be found in the Swagger page and the User Guide.

Yes, the Resource Browser in NIMP allows you to explore all unrestricted data available in NIMP through an interactive interface.

Refer the User Guide for detailed information. If you still have questions, email Rashmie Abeysinghe ([email protected])

Architectural Diagrams

Data Ecosystem Upstream Components (Blue Diagram)

The upstream BICAN data ecosystem workflow diagram shows how Specimen Portal facilitates data transfer across different ecosystem components.

Sequencing Library Workflow (Purple Diagram)

The sequencing library workflow diagram shows the detailed dataflow from Specimen Portal to Sequencing Portal, then to Seq Core and NeMO.

Resource Provenance Tracking (Sankey Diagram)

The BICAN resource-provenance visualization engine uses NHash identifier to identify, link, and track BICAN resource items from their source-point inception all the way to output data files. It uses the Sankey rendering library to visualize flow from donor ancestors to library aliquot descendants, through tissue region of interests (ROIs) as the intermediary, from any ancestor to any descendant and vice versa. It provides seamless linkage from resources in the Specimen Portal to those in the Sequencing Library Portal, whereby integrates the functional components of NIMP.

API Specification

The NIMP API suite, following the RESTful structure, allows users and systems to lookup various structured data, slab images, and annotations with API lookup calls. All BICAN resource types with NHash identifiers can be looked-up and retrieved using APIs, including, but not limited to: donor, slab, ROI, library, library pool, library aliquot, as well as all data elements (variable names) used in the implementation of NIMP (and mapped to other standardized codes and terms).

API Documentation

Publications

2025

Tissue-to-Bytes: A Catalytic Digital Twin Platform for Consortium-Scale Integration of Single-Cell Omics Data Across the BRAIN Initiative Cell Atlas Network

Authors

Shiqiang Tao, Xiaojin Li, Yan Huang, Rashmie Abeysinghe, Ling Tong, Shiwei Lin, Wei-Chun Chou, Erge Edgu-Fry, Kimberly A Smith, Lydia Ng, Licong Cui, Guo-Qiang Zhang

Tissue-to-Bytes: A Catalytic Digital Twin Platform for Consortium-Scale Integration of Single-Cell Omics Data Across the BRAIN Initiative Cell Atlas Network poster

Abstract

The NIH BRAIN Initiative Cell Atlas Network (BICAN) is a collaborative effort among neuroscientists, computational biologists, and data scientists to create reference brain cell atlases to be used by the research community as a molecular and anatomical foundational framework for the study of human brain function and disorders. Coordinated sharing and management of the scarce human brain tissue, across lifespans and among the eleven participating BICAN centers and laboratories with anatomical precision, is a formidable undertaking. Creating and operating the necessary data production pipelines with de novo metadata standards prospectively established to adhere to the highest possible levels of Findable, Accessible, Interoperable, and Reusable (FAIR) data principles, present unparalleled challenges that place BICAN into uncharted territories. A digital twin paradigm has been formulated and operationalized to manage advanced single-cell molecular techniques and complexity of data production workflows that are used in the BICAN consortium. The Neuroanatomy-anchored Information Management Platform (NIMP) implements the digital twin paradigm from conception to design, to production. NIMP is an agile, extensible, catalytic infrastructure for integrative and collaborative BICAN consortium-scale FAIR data generation. Digital-twin thinking ensures that NIMP provides tissue-to-bytes, end-to-end integration of data production pipelines spanning brain banks, laboratories, sequencing centers, and data archives. NIMP's digital twin characteristics are manifested in the coupling of real-world workflows occurring in the BICAN laboratories with their digital counterparts moving progressively through verifiable provenance lineage paths. The implementation of NIMP's digital twin features are grounded on advanced informatics strategies that include codification of anatomical contexts; standardized tissue request and sharing workflows, library preparation, sequencing, and single-cell omics data generation and deposition. These workflows and processes are governed by standardized Common Data Elements (CDEs); tracked by blockchain-inspired resource-identifiers (ID); ingested and edited using role-based access control (RBAC); and accessed by query-embedded dashboarding and atlas-enabled interactive resource exploration with dynamically rendered Sankey diagrams. In three years, NIMP has managed data and metadata for 762 human donors, 8,449 brain slabs, and 21,781 sequencing libraries across 11 laboratories, resulting in an estimated total of over 18 million cells for Basal Ganglia alone. The NIMP digital twin paradigm not only serves BICAN; it provides a blueprint for future-proof data coordination at consortium scale.

Public Link