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A tool for analyzing electrode tracks from slice histology

Philip ShamashiD, Matteo CarandiniiD, Kenneth D HarrisiD, Nicholas A. SteinmetziD

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Abstract

It is now possible to record from hundreds of neurons across multiple brain regions in a single electrophysiology experiment. An essential step in the ensuing data analysis is to assign recorded neurons to the correct brain regions. Brain regions are typically identified after the recordings by comparing images of brain slices to a reference atlas by eye. This introduces error, in particular when slices are not cut at a perfectly coronal angle or when electrode tracks span multiple slices. Here we introduce SHARP-Track, a tool to localize regions of interest and plot the brain regions they pass through. SHARP-Track offers a MATLAB user interface to explore the Allen Mouse Brain Atlas, register asymmetric slice images to the atlas using manual input, and interactively analyze electrode tracks. We find that it reduces error compared to localizing electrodes in a reference atlas by eye. See github.com/cortex-lab/allenCCF for the software and wiki.

Abstract summary

Claude Opus 5.5 · xhigh effort · 18 Oct 2026 · from the abstract · CC BY-NC 4.0

MATLAB tool registers histology slices to the Allen Mouse Brain Atlas and traces electrode tracks across them, reported to localize recording sites more accurately than eyeballing the atlas.

With hundreds of neurons recorded across many regions at once, every unit has to be assigned to a region, and that is normally done by eye against a reference atlas. Errors creep in when slices are not cut truly coronally or when a track runs through several slices, which a software registration and track reconstruction can address.

Key results

  1. ClaimedSHARP-Track provides a MATLAB interface that browses the Allen Mouse Brain Atlas, registers slice images to it with manual input, and traces an electrode track to report the regions it passes through.

    Registration is stated to handle asymmetric slice images, that is, slices not cut at a perfectly coronal angle, and track analysis is interactive; the abstract gives no registration algorithm or runtime. · Abstract

  2. ClaimedUsing the tool is reported to reduce localization error compared with placing electrodes in a reference atlas by eye.

    Stated as a finding, with no error metric, ground-truth reference, number of tracks or number of comparison raters given in the abstract. · Abstract

Methods, data and reproducibility

A MATLAB user interface for exploring the Allen Mouse Brain Atlas, registering histological slice images to it through manual input (including slices cut at asymmetric angles), and interactively reconstructing electrode tracks to list the brain regions they cross.

  • Allen Mouse Brain Atlas used as the reference for registration and region assignment · mouse
  • brain slice histology images containing electrode tracks · mouse
Methods & tools
SHARP-Track, MATLAB, Allen Mouse Brain Atlas
Software & environment
Distributed as a MATLAB user interface, with a wiki at the same repository; no MATLAB version or dependency list is stated.
Limitations (2)
  • The reported error reduction carries no numbers, no stated ground truth and no count of tracks or comparison raters, so its magnitude cannot be judged. · noted in this summary
  • Registration depends on manual input, so results will vary between users; variability between operators is not addressed in the available text. · noted in this summary

Read this if you run multi-region electrophysiology in mice and must assign recording sites to atlas regions from slice histology.

Citations
139

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