SCAN: The Spatiotemporal Cloud Atlas for Neural Cells

Mapping the Brain's Universe with Unprecedented Detail

Explore the Atlas

The Ultimate Brain Map: Introducing SCAN

The human brain is one of the most complex structures in the known universe, containing nearly 100 billion individual neurons working together to form the basis of every human thought, emotion, and behavior.

For centuries, scientists have struggled to understand how these constellations of cells form functional networks—until now. Recently, a revolutionary scientific breakthrough has emerged that promises to transform our understanding of the nervous system: SCAN, the Spatiotemporal Cloud Atlas for Neural Cells.

This groundbreaking database represents the most comprehensive effort to date to map the nervous system at an unprecedented level of detail. By combining cutting-edge technologies that reveal both what individual cells do and where they're located, SCAN provides researchers worldwide with an invaluable resource for exploring the links between molecules, cells, brain function, and disease.

This atlas doesn't just show us what's in the brain—it reveals how the nervous system develops, evolves, and sometimes malfunctions in conditions like Alzheimer's disease, autism, and depression 8 .

100B+

Neurons in Human Brain

10.7M

Cells Analyzed

900+

Species Covered

The Technology Revolution: How Scientists See the Invisible

Single-cell RNA Sequencing

scRNA-seq allows scientists to analyze the genetic activity of individual cells. Think of each cell as a factory that produces specific products based on its function—scRNA-seq lets us see exactly what each factory is producing.

This reveals the cellular diversity within tissues that appears uniform to the naked eye. The drawback? This method requires dissociating tissues, losing all information about where each cell originally resided 1 .

Spatial Transcriptomics

ST solves the location problem by capturing genetic information while preserving the spatial context of cells within tissues. It's like having a satellite map that shows not only what each factory produces but exactly where it's located in the city 1 .

SCAN represents the first database that comprehensively combines both approaches for the nervous system, creating a multidimensional atlas that reveals both what cells do and where they're located 7 .

How SCAN Combines Technologies

Single-cell RNA Sequencing

Reveals cellular diversity by analyzing genetic activity of individual cells

Spatial Transcriptomics

Preserves spatial context while capturing genetic information

SCAN Integration

Combines both approaches to create a comprehensive neural cell atlas

Building the Ultimate Brain Atlas: The Making of SCAN

Creating SCAN required a monumental effort of data collection and analysis. Researchers manually collected and analyzed high-quality scRNA-seq and ST data from an astonishing 10,679,684 cells from the nervous system.

10.7M

Cells Analyzed

900+

Species

100+

Neurological Diseases

Multi-omic

Datasets

Data Collection Process

The data collection process was meticulous. Researchers scoured scientific literature and public databases using specific keywords like "brain scRNAseq," "spinal cord scRNAseq," and "retina spatial transcriptomics" to identify relevant datasets. Each dataset had to meet strict quality criteria, including the availability of sample records, library construction methods, and cell type annotation information 1 .

Data Processing Pipeline

  • Quality filtering to remove low-quality cells
  • Cell type annotation using classic cell markers from original studies
  • Cross-species analysis to understand evolutionary relationships
  • Disease biomarker screening for neurological conditions
  • Developmental trajectory reconstruction to understand how cells mature and specialize 1

The result is a comprehensive, user-friendly database freely accessible to researchers worldwide at http://scanatlas.net 7 .

What SCAN Reveals: Surprising Discoveries About the Brain

Evolutionary Insights

By comparing brain regions across 12 species—including humans, mice, primates, and even fruit flies—researchers can now explore the evolutionary relationships between different nervous systems. This helps identify what makes the human brain unique while also revealing conserved patterns across species 1 .

Disease Connections

SCAN analysis has confirmed that genes linked to Alzheimer's disease tend to fall within DNA regulatory regions that are only accessible in microglia—the brain's primary immune cells. This validates the prominent role of microglia in Alzheimer's, which had been suggested by other studies 8 .

Cellular Heterogeneity

Perhaps one of the most surprising discoveries enabled by single-cell technologies is the incredible heterogeneity of brain cells. What once appeared to be uniform populations of "neuroepithelial cells" or "radial glia" actually contain numerous subtypes, each with potentially different functions during development 4 .

Specific Disease Findings

  • Basket cells are enriched for genetic risk factors for several disorders including schizophrenia, bipolar disorder, and epilepsy 8 .
  • Medium spiny neurons appear specifically linked to attention deficit/hyperactivity disorder (ADHD), suggesting promising new targets for future research 8 .

A Closer Look: The First Trimester Human Brain Atlas Experiment

One of the key experiments that demonstrates the power of single-cell approaches—and forms part of the foundation upon which SCAN builds—was published in Nature Neuroscience in 2021. This study created the first detailed atlas of early human brain development, highlighting surprising heterogeneity among human neuroepithelial cells and early radial glia 4 .

Methodology: Step-by-Step

Researchers obtained brain tissue from ten individuals during the first trimester of human development (gestational weeks 6-10), covering multiple brain regions including the telencephalon, diencephalon, midbrain, hindbrain, and cerebellum.

Using the droplet-based 10X Genomics Chromium platform, the team performed scRNA-seq on approximately 289,000 cells that passed quality control.

Computational algorithms grouped cells into clusters based on similar gene expression patterns. These clusters were then annotated into cell types using known marker genes.

The team used immunostaining and in situ hybridization to validate their findings and provide spatial context to the identified cell types 4 .

Results and Analysis: Rewriting the Textbook on Early Brain Development

The experiment yielded several groundbreaking findings that challenged conventional wisdom about early brain development:

Cell Type Abundance Key Features
Neuroepithelial Cells High in early stages Uniform appearance but transcriptomically diverse
Early Radial Glia Emerges during first trimester Express SOX2 and neurogenic genes
Mesenchymal-like Cells Highly prevalent early Non-neural origin
Early Neurons Present even in earliest samples Result from direct neurogenesis
Key Discoveries
  • The study revealed that the earliest stages of human brain development contain more cellular diversity than previously thought. The researchers identified nine distinct progenitor populations physically proximal to the telencephalon, rather than the more uniform population expected 4 .
  • Another surprising finding was the presence of neurons even in the earliest samples, suggesting that neurogenesis begins earlier than previously recognized. These early neurons likely result from "direct neurogenesis" from radial glia, bypassing the intermediate progenitor stage that becomes more common later in development 4 .
Gene/Genetic Factor Expression Pattern Potential Function
LHX5-AS1 Strongly enriched early, restricts to cortical plate May play repressive role to LHX5 protein
MEF2C High at earliest timepoints, diminishes, then re-expresses Regulator of early neuronal differentiation

The researchers also discovered that organoid systems—miniature lab-grown brain models—initially display low fidelity to neuroepithelial and early radial glia cell types but improve as neurogenesis progresses. This has important implications for how scientists use these models to study brain development and disease 4 .

The Scientist's Toolkit: Essential Reagents and Solutions for Brain Mapping

Creating detailed brain atlases like SCAN requires specialized reagents and tools. Here are some of the key solutions that enable this cutting-edge research:

Reagent/Tool Category Specific Examples Function in Research
Single-Cell RNA Sequencing Platforms 10X Genomics Chromium, Fluidigm C1 Partition individual cells for genetic analysis
Antibody Clones BD Biosciences Clone Comparison Tool Identify specific cell types through protein markers
Fluorochromes BD Horizon Brilliant Ultraviolet 615 Tag antibodies for detection in flow cytometry
Cell Preservation Solutions Organ preservation solutions, cryopreservation media Maintain tissue viability during processing
Spatial Transcriptomics Kits 10x Visium, Nanostring GeoMx Capture gene expression while preserving location
Genetic Engineering Tools CRISPR/Cas9, genetically encoded affinity reagents (GEARs) Precisely tag and manipulate endogenous proteins

Innovative Tools: GEARs

The development of genetically encoded affinity reagents (GEARs) represents a particularly innovative tool. These use small epitopes recognized by nanobodies and single-chain variable fragments to enable fluorescent visualization, manipulation, and even degradation of specific protein targets in living cells.

Unlike traditional methods, GEARs are multifunctional and adaptable, offering researchers unprecedented control when studying protein function in model organisms like zebrafish and mice 5 .

Reagent Management

Proper reagent management is also crucial for large-scale projects like SCAN. Laboratory information management systems (LIMS) help scientists track reagents, manage lot numbers, ensure quality control, and maintain inventory—essential logistics when coordinating research across multiple laboratories and institutions 6 .

The Future of Brain Science: Implications and Next Steps

SCAN represents more than just a snapshot of current knowledge—it's a dynamic resource that will continue to grow as new data emerges. The developers have committed to continuously updating the database with future published neural single-cell sequencing and spatial transcriptomics data, with plans to potentially integrate other multi-omics techniques as well 7 .

Medical Applications

The implications for medicine are profound. By providing comprehensive molecular maps of both healthy and diseased nervous tissue, SCAN enables researchers to:

  • Identify novel drug targets for neurological and psychiatric conditions
  • Understand the cellular mechanisms behind disease progression
  • Develop better diagnostic strategies based on cellular signatures
  • Compare human brain biology with model organisms more accurately

Explore SCAN Yourself

The database is freely accessible to researchers worldwide

Visit SCAN Database

As the scientific community continues to contribute to and utilize this resource, we move closer to solving some of the most stubborn mysteries in neuroscience. The atlas provides the foundation for a new era of brain research—one that acknowledges and explores the incredible diversity of cells that make up our nervous system.

The ultimate goal is not just to understand the brain in isolation, but to use that knowledge to develop effective treatments for the hundreds of millions of people worldwide affected by neurological and psychiatric disorders. With powerful resources like SCAN now available to researchers everywhere, that future may be closer than we think.

To explore the SCAN database for yourself, visit http://scanatlas.net 7 .

References