skills/claude-scientific-skills
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update to v1.3.1

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Andrey Fedorov
2026-02-11 09:42:22 -05:00
parent 2597540aa1
commit 5a471d9c36
1 changed files with 22 additions and 7 deletions
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scientific-skills/imaging-data-commons/SKILL.md
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@@ -3,7 +3,7 @@ name: imaging-data-commons
description: Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
license: This skill is provided under the MIT License. IDC data itself has individual licensing (mostly CC-BY, some CC-NC) that must be respected when using the data.
metadata:
version: 1.3.0
version: 1.3.1
skill-author: Andrey Fedorov, @fedorov
idc-index: "0.11.9"
idc-data-version: "v23"
@@ -20,20 +20,35 @@ Use the `idc-index` Python package to query and download public cancer imaging d
**Primary tool:** `idc-index` ([GitHub](https://github.com/imagingdatacommons/idc-index))
**Verify version and check current data scale:**
**CRITICAL - Check package version and upgrade if needed (run this FIRST):**
```python
import idc_index
REQUIRED_VERSION = "0.11.9" # Must match metadata.idc-index in this file
installed = idc_index.__version__
if installed < REQUIRED_VERSION:
print(f"Upgrading idc-index from {installed} to {REQUIRED_VERSION}...")
import subprocess
subprocess.run(["pip3", "install", "--upgrade", "--break-system-packages", "idc-index"], check=True)
print("Upgrade complete. Restart Python to use new version.")
else:
print(f"idc-index {installed} meets requirement ({REQUIRED_VERSION})")
```
**Verify IDC data version and check current data scale:**
```python
from idc_index import IDCClient
client = IDCClient()
# IMPORTANT: Always verify you're using the latest IDC data version
idc_version = client.get_idc_version()
print(f"IDC data version: {idc_version}") # Should be "v23"
# If version is older than v23, upgrade: pip install --upgrade idc-index
# Verify IDC data version (should be "v23")
print(f"IDC data version: {client.get_idc_version()}")
# Get collection count and total series
stats = client.sql_query("""
SELECT
SELECT
COUNT(DISTINCT collection_id) as collections,
COUNT(DISTINCT analysis_result_id) as analysis_results,
COUNT(DISTINCT PatientID) as patients,