Add probe geometry extraction for SpikeGLX Neuropixels data

[stevevanhooser]

Summary

Adds a new function to extract probe geometry information from SpikeGLX .meta files and convert it to the NDI probe_geometry document format. This enables proper spatial representation of electrode positions for Neuropixels recordings.

Key Changes

• New function probeGeometry(): Main entry point that reads a SpikeGLX .meta file and returns a structure with electrode positions and probe metadata matching the NDI probe_geometry specification
• Dual geometry parsing strategy:
  • Prefers snsGeomMap field for newer SpikeGLX versions (>= 20230202) which directly provides electrode coordinates
  • Falls back to computing geometry from imroTbl and probe type for older files
• Support for multiple probe types:
  • Neuropixels 1.0 (staggered 2-column, 20 µm pitch)
  • Neuropixels 2.0 single shank (2-column, 15 µm pitch)
  • Neuropixels 2.0 four shank (2-column, 15 µm pitch with 250 µm shank spacing)
  • Neuropixels Ultra (6 µm contacts)
• Helper functions:
  • find_meta_field(): Locates fields in meta struct accounting for name transformations
  • parse_snsGeomMap(): Parses the newer geometry format
  • compute_geometry_from_imro(): Reconstructs electrode positions from imroTbl entries
  • probe_type_info(): Maps probe types to model names and contact sizes

Implementation Details

• Output structure includes electrode positions (left-right, depth), shank IDs, contact dimensions, and probe metadata
• Coordinates are in micrometers with depth as the primary spatial dimension
• Front-back positions are set to zero (2D geometry)
• Robust error handling for malformed or missing geometry data
• Supports both 0-based (SpikeGLX) and 1-based (NDI) indexing conversions

https://claude.ai/code/session_01AiMXe9VfSzfRaNih6f7a76

[github-actions]

Test Results

108 tests  +16   108 ✅ +16   4s ⏱️ ±0s
 13 suites + 1     0 💤 ± 0 
  1 files   ± 0     0 ❌ ± 0 

Results for commit 79ab947. ± Comparison against base commit 284fdc1.

♻️ This comment has been updated with latest results.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 109 lines in your changes missing coverage. Please review.
✅ Project coverage is 28.54%. Comparing base (284fdc1) to head (b64d1c7).

Files with missing lines	Patch %	Lines
+ndr/+format/+neuropixelsGLX/probeGeometry.m	0.00%	109 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #93      +/-   ##
==========================================
- Coverage   29.24%   28.54%   -0.70%     
==========================================
  Files          91       92       +1     
  Lines        4469     4578     +109     
==========================================
  Hits         1307     1307              
- Misses       3162     3271     +109     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.