Scripts and utilities in active development. These tools work but may have bugs or rough edges. Use with caution and report issues.
Not production-ready. These tools are functional but have not been fully tested across all scenarios. If you encounter issues, please report them.
Why old FlyWire / Neuroglancer share links fail with Error retrieving metadata for volume graphene://…/fly_v31 — HTTP error 0, and how to fix them. Short version: it's the per-session prodv1 auth token (login / cookies / Brave Shields), not the link — the native viewer authenticates the source for you. Warm up the session by opening any scene first.
Parallel ID validator using ThreadPoolExecutor. Processes 5,000+ root IDs in under 2 minutes by parallelizing supervoxel lookups, then batching root lookups in a single API call. Uses the accurate supervoxel tracking method (not get_latest_roots).
python fast_validate_ids.py --input ids.txt
python fast_validate_ids.py --input ids.txt --output results.txt --workers 20
Updated version of fast_validate_ids with automatic path detection. Resolves the correct datastack path automatically, removing the need for manual configuration.
python fast_validate_ids_updated_auto_detect_path.py --input ids.txt --output results.txt
Parallel coordinate fetcher. Gets viewer-resolution coordinates for thousands of root IDs by parallelizing L2 chunk lookups, then batching L2 coordinate fetches. Output is tab-separated (root_id, x, y, z) ready to paste into Google Sheets.
python fast_get_coords.py --input ids.txt
python fast_get_coords.py --input ids.txt --output coords.tsv --workers 20
Complete workflow script: update IDs → get coordinates → output to file, clipboard, or Google Sheets. Combines multiple steps into one command.
python tracer_tools/scripts/full_pipeline.py --input ids.txt --output results.tsv
Batch ID validator for large datasets (1,000+ IDs). Processes in chunks with progress reporting. More robust than fast_validate_ids for very large batches and Windows environments.
python tracer_tools/scripts/validate_ids_batch.py --input ids.txt --output results.txt
Adds coordinate columns to CSV/TSV files. Reads root IDs from a specified column, fetches coordinates, and writes them to adjacent columns in-place.
python tracer_tools/scripts/process_file_column.py --input data.csv
Reads root IDs from a Google Sheet, fetches coordinates via CAVE, and writes the coordinates back to columns in the same sheet. Modifies in-place.
Safe mode version: creates a new worksheet with coordinate results rather than modifying the original sheet.
OAuth-based Google Sheets coordinate updater. Uses browser-based OAuth flow instead of service account credentials. Includes offset/limit support for processing sheets in batches.
python tracer_tools/scripts/sheets_coords_oauth.py --sheet "SHEET_ID" --offset 0 --limit 1000 --update-ids
Merges multiple Google Sheets into one. Useful for combining parallel batch outputs or consolidating results from multiple processing runs.
Interactive CLI for fetching coordinates for root IDs. Sequential processing (for small batches or one-off lookups).
python tracer_tools/scripts/get_coords_cli.py --datastack brain_and_nerve_cord --ids 720575941471915328
Interactive CLI for updating outdated segment IDs. Uses the accurate supervoxel method to track IDs through splits and merges.
python tracer_tools/scripts/update_ids_cli.py --datastack brain_and_nerve_cord --with-coords
Monitors real-time progress of running batch ID validation. Useful when processing large datasets with validate_ids_batch.py.
Saves your CAVE authentication token to the standard location. Run this once before using any CAVE-dependent scripts.