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. 2023 Oct 19;10(10):ENEURO.0328-23.2023.
doi: 10.1523/ENEURO.0328-23.2023. Print 2023 Oct.

YAEL: Your Advanced Electrode Localizer

Zhengjia Wang  1 , John F Magnotti  1 , Xiang Zhang  1 , Michael S Beauchamp  2
Affiliations

YAEL: Your Advanced Electrode Localizer

Zhengjia Wang et al. eNeuro. .

Abstract

Intracranial electroencephalography (iEEG) provides a unique opportunity to record and stimulate neuronal populations in the human brain. A key step in neuroscience inference from iEEG is localizing the electrodes relative to individual subject anatomy and identified regions in brain atlases. We describe a new software tool, Your Advanced Electrode Localizer (YAEL), that provides an integrated solution for every step of the electrode localization process. YAEL is compatible with all common data formats to provide an easy-to-use, drop-in replacement for problematic existing workflows that require users to grapple with multiple programs and interfaces. YAEL's automatic extrapolation and interpolation functions speed localization, especially important in patients with many implanted stereotactic (sEEG) electrode shafts. The graphical user interface is presented in a web browser for broad compatibility and includes an interactive 3D viewer for easier localization of nearby sEEG contacts. After localization is complete, users may enter or import data into YAEL's 3D viewer to create publication-ready visualizations of electrodes and brain anatomy, including identified brain areas from atlases; the response to experimental tasks measured with iEEG; and clinical measures such as epileptiform activity or the results of electrical stimulation mapping. YAEL is free and open source and does not depend on any commercial software. Installation instructions for Mac, Windows, and Linux are available at https://yael.wiki.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

None
Graphical abstract
Figure 1.
Figure 1.
Highlights of the YAEL 3D viewer. Users can freely rotate the brain to show lateral view (left panel), posterior view (middle panel), or top view (right panel). Gray scale shows MRI data (horizontal plane shows axial slice through MRI data; right hemisphere shows translucent cortical surface model). Colored volumes show different anatomic regions of interest. Colored spheres show electrode contacts on different sEEG shafts. Color scale set by user and can reflect anatomic location and categorical or continuous experimental or clinical results (Fig. 4).
Figure 2.
Figure 2.
Flowchart of YAEL workflow.
Figure 3.
Figure 3.
A, The manufacturer’s blueprint for an experimental subdural electrode strip, showing three miniature research contacts organized in a triangular pattern, located between two standard clinical contacts labeled “2” and “3.” B, If the CT is downsampled to the MRI resolution before viewing, the three miniature research contacts are not visible (black rectangle). C, In YAEL, the 3D viewer maintains the CT at the native resolution. The miniature research contacts are clearly visible (black rectangle).
Figure 4.
Figure 4.
A, Before localization (left panel), the viewer allows flexible 3D manipulation and visualization of the CT dataset (yellow color) and the MRI dataset (transparent cortical surface models). After localization (right panel), each electrode contact is visible as a sphere, with contacts on each sEEG shaft in a different color (the legend shows the code assigned to each shaft during implantation surgery). B, For automatic extrapolation, the user clicks the first two contacts of an sEEG shaft (shown) or a subdural electrode strip, then YAEL automatically localizes the remaining electrodes. C, For automatic interpolation, the user clicks on the first and last contact on a subdural electrode strip (shown) or an sEEG shaft. Clicking the “interpolate” button automatically localizes the intermediate electrodes. Interpolation succeeds despite the sharp curvature generated as the subdural strip conforms to the occipital pole.
Figure 5.
Figure 5.
YAEL creates high-quality visualizations from a variety of iEEG data. A, YAEL visualization of anatomic data. Colored volumes show different anatomic regions of interest (ROIs) from an atlas (legend at right). Spheres show sEEG electrode contacts. Colored contacts are located within an ROI, gray contacts are not in any ROI. B, YAEL visualization of categorical data. Contacts are colored by the results of electrical stimulation mapping. C, YAEL visualization of continuous data. Contacts are colored by the results of an analysis of iEEG power in two conditions, viewing faces and listening to voices. Only electrodes with a significant response are shown (nonsignificant contacts in gray). D, YAEL visualization of timeseries data. Each brain shows the power at one time point. Still frames show a movie where activity in each electrode was projected to the cortical surface. Alternately, only electrode activity can be shown, without projection to the cortical surface. Full videos available on software website. E, YAEL visualization of group data. Top row shows electrodes from multiple participants, visualized on a template brain (one color per participant). Bottom row shows summary data of number of contacts across all participants in each anatomic ROI. F, YAEL visualization of combination data. Six anatomic regions were selected; all electrodes within each region across participants were selected; and then each electrode was colored by the iEEG response to a stimulus.
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