Neuroscience

Installable Claude components for neural-data analysis, brain imaging, connectomics, electrophysiology, behavioral assays, and computational neuroscience.

10x Genomics Cloud MCP

MCP server · 10x Genomics · GA

Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.

ABCD Study Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the ABCD Study dataset, including download via NIMH Data Archive, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI

ABIDE Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the ABIDE (Autism Brain Imaging Data Exchange) dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data

ADHD-200 Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the ADHD-200 dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data

ADNI Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for ADNI data (fMRI + T1), including BIDS preparation, fMRIPrep preprocessing, and DK68 ROI pipeline.

AIBL Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the AIBL (Australian Imaging, Biomarkers and Lifestyle) dataset, including data access guidance, BIDS organization, and multimodal processing of sMRI and PET …

AIND Data MCP

MCP server · Allen Institute for Neural Dynamics · Beta

Official Allen Institute MCP server giving Claude query and NWB-introspection access to AIND’s V2 neuroscience data assets.

AOMIC Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the AOMIC (Amsterdam Open MRI Collection) dataset, including data access, BIDS organization, and multimodal processing of sMRI, rs-fMRI, and task-fMRI

ASL Perfusion MRI (Claude Skill)

Claude Skill · NeuroClaw · GA

Process Arterial Spin Labeling (ASL) perfusion MRI data including CBF (cerebral blood flow) quantification, ASL preprocessing (motion correction, partial volume correction, M0 normalization), or …

AnnData (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill teaching the AnnData annotated-data-matrix format used by Scanpy and scvi-tools for single-cell and other observation/feature matrices.

Anthropic PubMed Connector

MCP server · Anthropic · GA

Anthropic-managed NCBI literature search via PubMed and PubMed Central.

BGPT Paper Search (Claude Skill)

Claude Skill · K-Dense · GA

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.

BIDS (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for organizing, validating, and querying Brain Imaging Data Structure datasets — MRI, EEG, MEG, iEEG, PET, microscopy, behavioral, and 35 BIDS entities.

BOLD5000 Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the BOLD5000 dataset, including download, BIDS organization, and processing of task-fMRI data with visual image stimuli

BioContextAI Knowledgebase MCP

MCP server · BioContextAI · GA

Read-only MCP that unifies 14+ biomedical databases (Antibody Registry, UniProt, STRING, AlphaFold, KEGG, Open Targets) for immune and protein-context queries.

BioMCP

MCP server · GenomOncology · GA

Unified biomedical lookup across PubMed, ClinicalTrials.gov, MyVariant, and OpenFDA.

BioPython (Claude Skill)

Claude Skill · K-Dense · GA

Comprehensive molecular biology toolkit.

BioRender Connector

MCP server · BioRender · GA

Scientific-figure assembly from the 50,000+ BioRender icon and template library.

BioServices (Claude Skill)

Claude Skill · K-Dense · GA

Unified Python interface to 40+ bioinformatics services.

Biomni (Claude Skill)

Claude Skill · Stanford SNAP Lab · GA

General-purpose biomedical AI agent that plans and runs multi-step research workflows across genomics, drug discovery, and clinical analysis.

Brain Visualization (Claude Skill)

Claude Skill · NeuroClaw · GA

Visualize neuroimaging analysis results, including 3D brain connectivity networks, atlas-based regional activation summaries, or FreeSurfer cortical surface meshes with anatomical colors

BrainGNN (Claude Skill)

Claude Skill · NeuroClaw · GA

Run BrainGNN for fMRI phenotype prediction, including graph construction, training, and evaluation.

BrainNetworkTransformer (BNT) (Claude Skill)

Claude Skill · NeuroClaw · GA

Run BrainNetworkTransformer for fMRI phenotype prediction, including data loading, training, and evaluation.

COBRE Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the COBRE dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data for schizophrenia research

CONN Toolbox (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform advanced functional connectivity (ROI-to-ROI, seed-to-voxel, ICA) or effective connectivity (PPI, gPPI, DCM) analysis using the CONN Toolbox

Cam-CAN Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Cam-CAN (Cambridge Centre for Ageing and Neuroscience) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, task-fMRI, and MEG, phenotype …

Com-BrainTF (Claude Skill)

Claude Skill · NeuroClaw · GA

Run Com-BrainTF (Community-aware Brain Transformer) for fMRI phenotype prediction.

Composer

Plugin · Scripps AI Enablement · Beta

Turns a plain-language scientific problem into a grounded, runnable Claude solution composed from this catalog, reusing recipes and recommending autonomous systems.

Consensus Plugin

Claude Code Plugin · Consensus · GA

Consensus.app MCP plugin bringing AI-powered scientific literature search and evidence synthesis into Claude across all research areas.

DIPY (Claude Skill)

Claude Skill · NeuroClaw · GA

Execute concrete DIPY operations: load DWI (NIfTI+bvals+bvecs), optional masking, DTI fitting, compute FA/MD/AD/RD, and extract ROI statistics.

DMT-HAR-MED Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the DMT-HAR-MED dataset (ds006644), including download, BIDS organization, and processing of rs-fMRI data from a psychedelic intervention study

Database Lookup (Claude Skill)

Claude Skill · K-Dense · GA

Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.

Dictionary Learning (rs-fMRI) (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform resting-state network decomposition using DictLearning.

Diffusion MRI (DWI) (Claude Skill)

Claude Skill · NeuroClaw · GA

Preprocess diffusion MRI / DWI data, compute diffusion metrics (FA/MD/AD/RD, etc.), extract ROI-wise diffusion features, or run tractography/connectome-related workflows

EEG Processing (Claude Skill)

Claude Skill · NeuroClaw · GA

Load, preprocess, epoch, filter, or extract features from EEG data (resting-state, task-based, BCI, clinical, motor imagery, emotion, epilepsy, fatigue, etc.)

Ensembl MCP Server

MCP server · effieklimi · GA

MCP server over the Ensembl REST API for gene/transcript lookup, sequence retrieval, variant consequences, comparative genomics, and assembly lift-over.

FM-APP (Claude Skill)

Claude Skill · NeuroClaw · GA

Run FM-APP for phenotype prediction using fMRI ROI features and optional sMRI features.

FSL (Claude Skill)

Claude Skill · NeuroClaw · GA

Process neuroimaging data with FSL (FMRIB Software Library), covering structural MRI, functional MRI (fMRI), and diffusion MRI (dMRI/DTI)

Process structural MRI data (T1w, T2w, FLAIR, etc.) with FreeSurfer, especially for cortical/subcortical segmentation, surface reconstruction, parcellation, cortical thickness, volume statistics, or full recon-all pipeline

GLM (Task-fMRI) (Claude Skill)

Claude Skill · NeuroClaw · GA

Run a classical General Linear Model (GLM) for task-evoked fMRI activation analysis.

HCP Early-Psychosis Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the HCP Early Psychosis (HCP-EP) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI

HCP Pipelines (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform high-quality, HCP-style preprocessing of multimodal MRI data (structural, functional, diffusion) using the official HCP Pipelines

HCP Young-Adult Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the HCP Young Adult (HCP-YA / HCP1200) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI

HCP-Aging Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the HCP Aging (HCP-A) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI

HCP-Development Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the HCP Development (HCP-D) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI

Healthy Brain Network (HBN) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Healthy Brain Network (HBN) dataset, including download, BIDS organization, and multimodal processing of sMRI, dMRI, rs-fMRI, task-fMRI, and EEG data

Hierarchical Parcellation (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform brain parcellation using Hierarchical clustering.

Hypothesis Generation (Claude Skill)

Claude Skill · K-Dense · GA

Structured hypothesis formulation from observations.

IBGNN (Claude Skill)

Claude Skill · NeuroClaw · GA

Run IBGNN (Interpretable Brain Graph Neural Network) for fMRI phenotype prediction.

ICA Decomposition (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform resting-state network decomposition using ICA.

IXI Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the IXI (Information eXtraction from Images) dataset, including data download, BIDS organization, and multimodal processing of T1w, T2w, and MRA

K-means Parcellation (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform brain parcellation using K-means.

LG-GNN (Claude Skill)

Claude Skill · NeuroClaw · GA

Run LG-GNN (Local-to-Global GNN) for fMRI phenotype prediction.

Literature Review (Claude Skill)

Claude Skill · K-Dense · GA

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).

MEG Processing (Claude Skill)

Claude Skill · NeuroClaw · GA

Process MEG (magnetoencephalography) data including source localization, time-frequency analysis, connectivity analysis, sensor-level preprocessing, or MEG-specific feature extraction

MNE-Python (EEG) (Claude Skill)

Claude Skill · NeuroClaw · GA

Execute concrete MNE-Python operations for EEG loading, preprocessing, filtering, artifact removal, epoching, frequency-band analysis, or feature extraction.

MS Lesion Segmentation Challenge Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Longitudinal MS Lesion Segmentation Challenge dataset, including data validation, multimodal processing of T1w, T2w, FLAIR, and PD, lesion segmentation, and …

Motor Neuron Disease (MND) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Motor Neuron Disease (MND) dataset from OpenNeuro ds005874, including BIDS validation, multimodal processing of rs-fMRI and task-fMRI, phenotype extraction, and …

NIFD (Frontotemporal Dementia) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Neuroimaging in Frontotemporal Dementia (NIFD) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, and dMRI, phenotype extraction, and QC integration

Natural Scenes Dataset (NSD) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Natural Scenes Dataset (NSD), including data access, BIDS validation, multimodal processing of task-fMRI and structural MRI, stimulus metadata extraction, and …

NeuroHarmonize (ComBat) (Claude Skill)

Claude Skill · NeuroClaw · GA

Remove site/scanner/batch effects from neuroimaging features before running downstream models, run mega-analysis across multiple datasets, or evaluate models with leave-site-out / site-stratified protocols

NeuroKit2 (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for biosignal processing — ECG, EEG, EDA, RSP, PPG, EMG, and EOG analysis including HRV, event-related responses, and multi-modal physiological insights.

NeuroSTORM (Claude Skill)

Claude Skill · NeuroClaw · GA

Run the NeuroSTORM multi-model fMRI platform: preprocessing, pretraining (MAE or contrastive), fine-tuning, inference, or benchmarking.

Neuropixels-Analysis (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for end-to-end Neuropixels analysis — SpikeGLX/Open Ephys/NWB loading, preprocessing, motion correction, and Kilosort4/SpykingCircus2/Mountainsort5 spike sorting.

Neurosift Tools MCP

MCP server · Flatiron Institute · Beta

MCP server that lets Claude search DANDI/OpenNeuro and introspect NWB neurophysiology files, plus semantic search over PyNWB docs.

NiBabel (Claude Skill)

Claude Skill · NeuroClaw · GA

NeuroClaw needs concrete nibabel operations for neuroimaging files: loading and validating NIfTI images, inspecting shapes and affine matrices, saving derived images, converting voxel coordinates …

Nilearn (Claude Skill)

Claude Skill · NeuroClaw · GA

Execute concrete Nilearn operations: ROI/atlas time-series extraction, confounds handling (fMRIPrep), seed-based connectivity maps, ROI-to-ROI connectivity matrices, and optional GLM/decoding utilities.

OASIS Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the OASIS (Open Access Series of Imaging Studies) dataset, including BIDS validation, multimodal processing of sMRI, and phenotype extraction for aging …

OpenNeuro MCP

MCP server · Quentin Cody (community) · Beta

Community MCP server giving Claude GraphQL access to the OpenNeuro archive of MRI, MEG, EEG, iEEG, and ECoG datasets.

PET Processing (Claude Skill)

Claude Skill · NeuroClaw · GA

Process PET neuroimaging data including spatial normalization to T1w/MNI space, SUVR computation, reference region quantification, partial volume correction, or tracer-specific workflows (PiB amyloid, FDG …

PNC Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Philadelphia Neurodevelopmental Cohort (PNC) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, task-fMRI, and dMRI, phenotype extraction, and QC integration

PPMI Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Parkinson’s Progression Markers Initiative (PPMI) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, and dMRI, phenotype extraction, and QC integration

Paper Lookup (Claude Skill)

Claude Skill · K-Dense · GA

Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.

QSIPrep (Claude Skill)

Claude Skill · NeuroClaw · GA

Run QSIPrep (BIDS App) for diffusion MRI (DWI) preprocessing with best-practice workflows (topup/eddy, denoising/unringing options, susceptibility/motion correction, coregistration/normalization, QC reports) on BIDS datasets.

REST-meta-MDD Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the REST-meta-MDD (Resting-State Meta-Major Depressive Disorder) dataset, including BIDS validation, processing of rs-fMRI, phenotype extraction, and QC integration

Run Models (NeuroClaw) (Claude Skill)

Claude Skill · NeuroClaw · GA

Run phenotype-prediction models, browse model cards, map model inputs/outputs, or choose an execution route for fMRI/sMRI based models.

SEED-IV (EEG Emotion) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the SEED-IV (SJTU Emotion EEG Dataset - 4 emotions) dataset, including EEG validation, preprocessing, feature extraction, and emotion classification

SEED-VIG (EEG Vigilance) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the SEED-VIG (SJTU Emotion EEG Dataset - Vigilance) dataset, including EEG validation, preprocessing, feature extraction, and vigilance/fatigue detection

SVM Classifier (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform disease classification with SVM.

Scanpy-MCP

MCP server · scmcphub · GA

MCP server wrapping Scanpy so Claude can run end-to-end single-cell RNA-seq analyses (QC, clustering, DE, plotting) from natural language.

Scholar Gateway Connector (Wiley)

MCP server · Wiley · Beta

Wiley remote connector for peer-reviewed scholarly content — 3M+ articles, 300+ Life Sciences journals.

Scientific Brainstorming (Claude Skill)

Claude Skill · K-Dense · GA

Creative research ideation and exploration.

Scientific Critical Thinking (Claude Skill)

Claude Skill · K-Dense · GA

Evaluate scientific claims and evidence quality.

Signal Detrending (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform neuroimaging signal denoising with classical detrending methods.

SpaceNet Classifier (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform disease classification with SpaceNet.

SpikeInterface (Claude Skill)

Claude Skill · SciAgent · GA

Unified Python framework for extracellular electrophysiology.

SpikeLab

Claude Skill · Braingeneers · Beta

Agent-skill suite for multi-electrode-array spike-train analysis and spike sorting (Kilosort2/4, RT-Sort), with an optional built-in MCP server.

Structural MRI (sMRI) (Claude Skill)

Claude Skill · NeuroClaw · GA

Process structural MRI (sMRI) such as T1w/T2w/FLAIR for brain extraction, bias correction, tissue segmentation (GM/WM/CSF), registration to MNI, cortical/subcortical parcellation, cortical thickness/volumetry (FreeSurfer), HCP-style …

Synapse.org Connector

MCP server · Sage Bionetworks · GA

Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.

Temporal Filtering (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform neuroimaging signal denoising with classical temporal filtering methods.

ToolUniverse

MCP server · Zitnik Lab (Harvard Medical School) · MIT Lincoln Laboratory · GA

Harvard / MIT MCP server bundling 600+ vetted scientific tools — literature, chemistry, omics, clinical trials — for AI-scientist-style hypothesis exploration.

Transdiagnostic Connectome Project (TCP) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the Transdiagnostic Connectome Project (TCP) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, and dMRI, phenotype extraction, and QC integration

UCLA CNP Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

End-to-end workflow for the UCLA CNP (Consortium for Neuropsychiatric Phenomics) dataset, including BIDS validation, multimodal processing of sMRI, task-fMRI, and dMRI, phenotype extraction, and …

UK Biobank (Brain) Pipeline (Claude Skill)

Claude Skill · NeuroClaw · GA

Analyze already available UK Biobank data for brain-related research, including neurological outcomes, cognitive phenotypes, brain MRI derived phenotypes, survival analysis, subgroup analysis, propensity score …

WMH Segmentation (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform automated white matter hyperintensity (WMH) segmentation on structural MRI data using the MARS-WMH nnU-Net model.

allenbrain-mcp

MCP server · maflot (community) · Alpha

Community MCP wrapper exposing Allen Brain Atlas RMA queries, cell-types, mouse connectivity, ontologies, and image/grid downloads to Claude.

bio-research (Claude Code Plugin)

Claude Code Plugin · Anthropic · GA

Umbrella plugin bundling 5 analysis skills and ~10 MCP connectors (PubMed, BioRender, ChEMBL, Synapse, Wiley, Open Targets, Benchling, etc.) for preclinical R&D.

dcm2niix (DICOM → NIfTI) (Claude Skill)

Claude Skill · NeuroClaw · GA

Convert DICOM files or folders to NIfTI format (.nii or .nii.gz), extract neuroimaging volumes from clinical DICOM series (MRI, CT, PET, etc.), prepare raw …

fMRI Processing (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform fMRI preprocessing, first-level analysis, ROI extraction, functional connectivity, effective connectivity, or atlas-based alignment to MNI152 space using either fMRIPrep, HCP-style pipelines, or CONN Toolbox

fMRIPrep (Claude Skill)

Claude Skill · NeuroClaw · GA

Perform standardized preprocessing of functional MRI (fMRI) and anatomical MRI data using fMRIPrep

nextflow-development

Claude Skill · Anthropic · GA

Runs nf-core rnaseq, sarek, and atacseq pipelines on local FASTQ or GEO/SRA inputs.

nii2dcm (NIfTI → DICOM) (Claude Skill)

Claude Skill · NeuroClaw · GA

Convert NIfTI files (.nii or .nii.gz) to DICOM format, create DICOM series from processed neuroimaging results, write segmentation/registration/analysis outputs back to DICOM for PACS …

scVelo (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for RNA-velocity analysis with scVelo — estimates cell-state transitions from unspliced/spliced mRNA counts, infers trajectories, latent time, and driver genes.

scientific-problem-selection

Claude Skill · Anthropic · GA

Structured framework for research project ideation, risk assessment, and troubleshooting, based on Fischbach & Walsh (Cell 2024).

scvi-tools

Claude Skill · Anthropic · GA

Deep-learning workflows for scVI, scANVI, totalVI, MultiVI, PeakVI, DestVI, and related scvi-tools models for single-cell omics.

single-cell-rna-qc

Claude Skill · Anthropic · GA

scverse MAD-based QC for .h5ad and 10x .h5 single-cell RNA-seq inputs.

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