Scitex Dataset

When the host has multiple Python interpreters — e.g. a pre-built agent venv at /opt/venv-agent, a Spartan module load Python/3.11.3, or an existing ~/.venv you want to leave alone — point uv at the exact interpreter you want with --python:

# install into a specific venv WITHOUT touching project-local .venv
uv pip install --python /opt/venv-agent/bin/python "scitex-dataset[all]"

# one-shot CLI run under that interpreter
uv run --python /opt/venv-agent/bin/python scitex-dataset list-python-apis

# install the CLI as a tool, pinned to the same interpreter
uv tool install --python /opt/venv-agent/bin/python "scitex-dataset[mcp]"

# in a downstream script that bootstraps scitex-dataset, honour
# SCITEX_PYTHON if the caller sets it:
SCITEX_PYTHON="${SCITEX_PYTHON:-/opt/venv-agent/bin/python}"
uv pip install --python "$SCITEX_PYTHON" "scitex-dataset[all]"

The Makefile honours PYTHON=:

PYTHON=/opt/venv-agent/bin/python make install

See issue #38.

from scitex_dataset import (
    openneuro_fetch, dandi_fetch, huggingface_search,
    filter_results, list_sources,
    db_build, db_search,
)

# 1) Fetch from any catalog source — every <src>_fetch alias is 1:1
#    with the dataset_<src>_fetch MCP tool.
records = openneuro_fetch(max_datasets=100)

# 2) Filter + rank in memory.
top = filter_results(
    records, modality="eeg", min_subjects=20,
    sort_by="downloads", limit=10,
)

# 3) Search HuggingFace Hub directly (on-demand, no catalog).
hf_hits = huggingface_search("biology", limit=20)

# 4) Build the local SQLite + FTS5 index for offline queries.
db_build()
db_search("Alzheimer EEG")

# 5) Inspect the supported sources.
list_sources()["count"]   # 11

Full API reference

scitex-dataset --help-recursive             # Show all commands

# Grammar: scitex-dataset <domain> <dataset> <action>
scitex-dataset neuroscience openneuro fetch -n 100 -o datasets.json -v
scitex-dataset neuroscience dandi fetch -n 50 -o dandi.json -v
scitex-dataset neuroscience physionet fetch -n 50 -v
scitex-dataset general zenodo fetch -q "neuroscience" -n 20

# HuggingFace (general/huggingface noun-group has 4 verbs)
scitex-dataset general huggingface fetch Anthropic/BioMysteryBench-full
scitex-dataset general huggingface search "biology" -n 20 --json

# Local database
scitex-dataset db build                     # index all catalog sources
scitex-dataset db search "epilepsy EEG"     # full-text search
scitex-dataset db show-stats                # show statistics

# Introspection
scitex-dataset list-python-apis -v          # list Python API tree
scitex-dataset mcp list-tools -v            # list MCP tools

Full CLI reference

AI agents can discover and query neuroscience datasets autonomously.

_{Table 2. 21 MCP tools across catalog fetchers, HuggingFace, the local index, and skill introspection. Every MCP tool has a matching public Python alias (e.g. scitex_dataset.openneuro_fetch).}

scitex-dataset mcp start

Full MCP specification

Skills provide workflow-oriented guides that AI agents query to discover capabilities and usage patterns.

scitex-dataset skills list              # List available skill pages
scitex-dataset skills get SKILL         # Show main skill page
scitex-dev skills export --package scitex-dataset  # Export to Claude Code