espeare/stereoplan: v1.0.0-thesis

<html> <body> <html><head></head><body><h1>StereoPlan v1.0.0-thesis</h1> <p><strong>Release date:</strong> 2026-06-04</p> <p>This is the first stable release of StereoPlan, developed to support stereotaxic probe planning for non-human primate electrophysiology research. The software was created as a purpose-built planning tool and is archived here to support reproducibility of the associated thesis work.</p> <hr> <h2>Overview</h2> <p>StereoPlan is a desktop application for planning single-unit recording probe trajectories through a parcellated brain volume. It provides an interactive 3-D viewport, coronal slice visualisation, and tissue-sequence analysis along candidate probe paths, enabling researchers to identify optimal entry points and insertion depths prior to surgery.</p> <hr> <h2>Features in this release</h2> <h3>Probe placement</h3> <ul> <li>Interactive 3-D brain surface rendered via PyVista; click-to-place probe entry on a configurable chamber aperture disc</li> <li>Adjustable insertion depth via slider with preset (10 mm, 15 mm) and custom maximum depth options</li> <li>Real-time coronal MRI slice with CHARM cytoarchitectonic overlay at the probe's anterior-posterior coordinate</li> <li>Probe trajectory drawn on the coronal slice with entry and tip markers</li> </ul> <h3>Bend-tolerance modelling</h3> <ul> <li>Cylindrical sweep around the probe axis models worst-case tissue contact given probe flex</li> <li>Adjustable bend radius (0–5 mm) via spinner control</li> <li>Tissue regions reported separately for the central path and the bend envelope, with the corridor visualised on the coronal slice</li> </ul> <h3>Entry search (Find Entry mode)</h3> <ul> <li>Vectorised heatmap computation across all entry points in the chamber aperture or grid insert; identifies the shallowest depth at which each entry reaches a user-selected target region</li> <li>Results displayed as a colour-coded 3-D heatmap and a sortable table (shallowest insertion depth first)</li> <li>Click any table row to preview the corresponding probe trajectory</li> </ul> <h3>Grid insert support</h3> <ul> <li>Built-in presets for Crist-style electrode grid inserts (Crist A and Crist B), with correct hole geometry and spacing</li> <li>Custom grid mode with user-defined hole spacing and radius</li> <li>Independent roll control rotates the insert within the chamber plane without altering probe direction</li> <li>Hole labels (H000 format) carried through to the results table and exports to match physical insert labelling</li> </ul> <h3>Chamber controls</h3> <ul> <li>Chamber centre repositionable in X, Y, Z (mm, world space)</li> <li>Pitch and yaw tilt up to ±30°; debounced input prevents excessive recomputation during slider dragging</li> <li>Configurable aperture radius</li> </ul> <h3>Export</h3> <ul> <li>One-click export from either tab writes a composite PNG (3-D view + coronal slice or heatmap table) and a plain-text README containing all planning parameters: chamber geometry, probe entry and tip coordinates, insertion depth, direction vector, and full tissue-sequence annotation</li> </ul> <hr> <h2>Dependencies</h2> Package | Role -- | -- numpy | Numerical arrays, coordinate transforms, vectorised heatmap nibabel | NIfTI volume loading and affine handling scikit-image | Marching-cubes brain surface extraction scipy | 3-D rotation utilities pyvista | 3-D rendering and interactive picking matplotlib | Colormap lookup for CHARM label overlay PySide6 | GUI framework (Qt6 bindings) <p>Python 3.10 or later is required.</p> <hr> <h2>Limitations and scope</h2> <p>This release is scoped to the specific atlas and experimental setup described in the accompanying thesis. Hard-coded path defaults in <code>core.py</code> and the empirical coordinate alignment transform are specific to that configuration and should be updated for use in other contexts. No automated test suite is included in this release.</p> <hr> <h2>Citation</h2> <p>If you use StereoPlan in your work, please cite this release directly:</p> <blockquote> <p><strong>Emily Sperry</strong> (2026). <em>StereoPlan</em> (v1.0.0). GitHub. https://github.com/espeare/stereoplan/releases/tag/v1.0.0-thesis</p> </blockquote></body></html> </body> </html>

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