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Copilot AI commented Nov 11, 2025

When a manipulator connects via Ephys Link, it sets the reference coordinate to 0,0,0, causing the probe to appear displaced from its expected location. Users need to understand this behavior and how to correct it.

Changes

Updated step 6 in the "Mirror the Positions of in vivo Probes in Pinpoint" section to:

  • Explain that connection resets the reference coordinate to 0,0,0
  • Warn that the probe position will appear to shift
  • Clarify options to sync coordinates: manually set via text boxes or touch probe to bregma and use the home button

The updated instruction now reads:

Upon connection, the manipulator will set the default reference coordinate to 0,0,0, so the probe may look like it moved away from your expected location. You can manually set the reference coordinate through the text boxes, or you can touch the in vivo probe to bregma and use the home button (label 6.1) to re-read the manipulator's position and sync the reference coordinate.

Original prompt

update ephys link mirror probe instructions to say that once a manipulator connects it will set the default reference coordinate to 0,0,0 so the probe may look it moved away from your expected location. then keep the rest of the instructions to manually set the reference coordinate or touch the in vivo probe to bregma and use the home button to sync the reference cooridnate


💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

Copilot AI changed the title [WIP] Update ephys link mirror probe instructions for coordinate reference Clarify reference coordinate reset behavior when connecting manipulators Nov 11, 2025
Copilot finished work on behalf of kjy5 November 11, 2025 00:27
Copilot AI requested a review from kjy5 November 11, 2025 00:27
@kjy5 kjy5 marked this pull request as ready for review November 11, 2025 00:30
@kjy5 kjy5 enabled auto-merge (squash) November 11, 2025 00:30
@kjy5 kjy5 merged commit c78887b into main Nov 11, 2025
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@kjy5 kjy5 deleted the copilot/update-mirror-probe-instructions branch November 11, 2025 00:31
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2 participants