Projects

Research projects and initiatives focused on understanding brain structure, function, and neurodegenerative diseases.

Overview

Major neuroscience research projects have transformed our understanding of brain structure and function.

Key Categories

Brain Atlases: Comprehensive maps of brain anatomy and gene expression:

• Allen Brain Atlas series
• BrainSpan Atlas
• Human Connectome Project
• Julich-Brain Atlas

Cell Type Projects: Detailed characterization of neuronal and glial cell types:

• Allen Brain Cell Atlas
• BICCN
• Human Cell Atlas

Observatory Programs: Systematic studies of brain cell types and connectivity:

• Allen Brain Observatory
• MICrONS
• OpenScope

Clinical Studies: Longitudinal studies of disease progression:

• ADNI
• SEA-AD
• PPMI

All Pages (22)

Brain Atlases

• [Allen Brain Atlas Data Portal](/projects/brain-atlas)
• [Allen Brain Atlas: Cell Types Database](/projects/cell-types)
• [Allen Brain Cell Atlas](/projects/allen-brain-cell-atlas)
• [Allen Human Brain Atlas](/projects/human-brain-atlas)
• [Allen Mouse Brain Atlas](/projects/mouse-brain-atlas)
• [Allen Mouse Brain Connectivity Atlas](/projects/connectivity-atlas)
• [BrainSpan Atlas](/projects/brainspan)
• [Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD)](/projects/sea-ad)

Brain Observatory Programs

• [Allen Brain Observatory](/projects/allen-brain-observatory)
• [MindScope Program](/projects/mindscope)
• [MICrONS](/projects/microns)
• [OpenScope](/projects/openscope)

Cell Type Projects

...

Research projects and initiatives focused on understanding brain structure, function, and neurodegenerative diseases.

Overview

Major neuroscience research projects have transformed our understanding of brain structure and function.

Key Categories

Brain Atlases: Comprehensive maps of brain anatomy and gene expression:

• Allen Brain Atlas series
• BrainSpan Atlas
• Human Connectome Project
• Julich-Brain Atlas

Cell Type Projects: Detailed characterization of neuronal and glial cell types:

• Allen Brain Cell Atlas
• BICCN
• Human Cell Atlas

Observatory Programs: Systematic studies of brain cell types and connectivity:

• Allen Brain Observatory
• MICrONS
• OpenScope

Clinical Studies: Longitudinal studies of disease progression:

• ADNI
• SEA-AD
• PPMI

All Pages (22)

Brain Atlases

• [Allen Brain Atlas Data Portal](/projects/brain-atlas)
• [Allen Brain Atlas: Cell Types Database](/projects/cell-types)
• [Allen Brain Cell Atlas](/projects/allen-brain-cell-atlas)
• [Allen Human Brain Atlas](/projects/human-brain-atlas)
• [Allen Mouse Brain Atlas](/projects/mouse-brain-atlas)
• [Allen Mouse Brain Connectivity Atlas](/projects/connectivity-atlas)
• [BrainSpan Atlas](/projects/brainspan)
• [Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD)](/projects/sea-ad)

Brain Observatory Programs

• [Allen Brain Observatory](/projects/allen-brain-observatory)
• [MindScope Program](/projects/mindscope)
• [MICrONS](/projects/microns)
• [OpenScope](/projects/openscope)

Cell Type Projects

• [BICCN: Brain Initiative Cell Census Network](/projects/biccn)
• [BICAN: Brain Institute for Neural Genetics](/projects/bican)
• [Cell Types Database](/projects/cell-types)

Clinical Studies

• [Alzheimer's Disease Neuroimaging Initiative (ADNI)](/projects/adni)

NeuroWiki Internal

• [NeuroWiki Dashboard](/projects/neurowiki-dashboard)
• [NeuroWiki Progress](/projects/neurowiki-progress)
• [NeuroWiki Work Queue](/projects/neurowiki-work-queue)
• [Page Suggestions](/projects/page-suggestions)
• [What to Work On — NeuroWiki Decision Guide](/projects/what-to-work-on)

Rankings & Overviews

• [Neuroscience Project Rankings](/projects/rankings)
• [Neuroscience Projects Overview](/projects/overview)

Related Pages

• [Datasets](/datasets) — Data resources from these projects

Related Sections

• [Institutions](/institutions) — Institutions leading research projects
• [Researchers](/researchers) — Researchers involved in projects
• [Funding](/investment) — Funding and grant information

See Also

• [Alzheimer's Disease](/diseases/alzheimers-disease)
• [Parkinson's Disease](/diseases/parkinsons-disease)

External Links

• [PubMed](https://pubmed.ncbi.nlm.nih.gov/)
• [KEGG Pathways](https://www.genome.jp/kegg/pathway.html)

Related Hypotheses

From the [SciDEX Exchange](/exchange) — scored by multi-agent debate

• [Transcriptional Autophagy-Lysosome Coupling](/hypothesis/h-ae1b2beb) — <span style="color:#81c784;font-weight:600">0.72</span> · Target: FOXO1
• [Enhancing Vagal Cholinergic Signaling to Restore Gut-Brain Anti-Inflammatory Communication](/hypothesis/h-a4e259e0) — <span style="color:#81c784;font-weight:600">0.65</span> · Target: CHRNA7
• [Context-Dependent CRISPR Activation in Specific Neuronal Subtypes](/hypothesis/h-63b7bacd) — <span style="color:#81c784;font-weight:600">0.62</span> · Target: Cell-type-specific essential genes
• [DNMT1-Targeting Antisense Oligonucleotide Reset](/hypothesis/h-782e55f6) — <span style="color:#ffd54f;font-weight:600">0.45</span> · Target: DNMT1

Related Analyses:

• [Autophagy-lysosome pathway convergence across neurodegenerative diseases](/analysis/SDA-2026-04-01-gap-011) &#x1f504;
• [Epigenetic clocks and biological aging in neurodegeneration](/analysis/SDA-2026-04-01-gap-v2-bc5f270e) &#x1f504;
• [Tau propagation mechanisms and therapeutic interception points](/analysis/SDA-2026-04-02-gap-tau-prop-20260402003221) &#x1f504;

Neurodegeneration Focus in SciDEX

The projects indexed here collectively form the empirical backbone of SciDEX neurodegeneration research. The Allen Brain Atlas series provides the baseline gene expression landscape against which disease-altered transcriptomes are compared. The Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) extends this to single-cell resolution in AD-affected tissue, revealing cell-type-specific vulnerabilities. ADNI (Alzheimer's Disease Neuroimaging Initiative) provides the longitudinal clinical and imaging data used to validate neurodegeneration biomarkers and disease staging systems [@PMID:22996553].

Collectively, these projects have established that neurodegeneration involves convergent failures across multiple cell types — neurons, microglia, astrocytes, oligodendrocytes — rather than primary neuronal disease, reshaping therapeutic strategies toward multi-target and immunomodulatory approaches. PPMI (Parkinson's Progression Markers Initiative) plays an analogous role for Parkinson's disease, enabling biomarker-driven patient stratification.

Cross-Links

• [[Allen Human Brain Atlas]] — Foundational transcriptomic reference for the brain
• [[Seattle Alzheimer's Disease Brain Cell Atlas]] — Single-cell AD disease atlas
• [[ADNI]] — Alzheimer's Disease Neuroimaging Initiative longitudinal cohort
• [[PPMI]] — Parkinson's Progression Markers Initiative biomarker study
• [[Neurodegeneration Biomarkers]] — Key outputs from these projects