3D atlas locations of rat brain injection sites and section images from tract tracing experiments involving the orbitofrontal cortex (v1)

This dataset provides coordinates describing 3D locations in the Waxholm Space (WHS) rat brain atlas of injection sites (n=30) placed in female Sprague-Dawley rats (n=26). The source dataset ([Kondo et al., 2022](https://doi.org/10.25493/2MX9-3XF)) contains coronal microscopic section images (PNG, TIFF and MRXS files), and JSON coordinate files resulting from the registration of the images to the [Waxholm Space Rat brain atlas](https://scicrunch.org/resolver/RRID:SCR_017124) v4 using the [QuickNII](https://search.kg.ebrains.eu/?facet_type[0]=Dataset&category=Software&q=quicknii#d8d0abf0-aa7a-4be9-8fe4-34b36db7a039) and [VisuAlign](https://search.kg.ebrains.eu/?facet_type[0]=Dataset&category=Software&q=visualign#b20533ea-02a3-46a8-bbf4-f66036567233) software. The location of the injection site and the section images within an experiment was transformed to 3D atlas sphere and polygon representations, respectively, using the Locare workflow. To determine the injection site location, the tissue section image with the injection site of the largest extent (the image showing the highest density of tracer solution) was selected for evaluation. The sphere’s centroid coordinate and radius was estimated using the original MRXS files in combination with the atlas-registered TIFF files. The polygons were derived from the QuickNII and VisuAlign JSON files by script. The JSON files shared here follow the locareSphere or locarePolygon schema ([https://github.com/Neural-Systems-at-UIO/LocareJSON](https://github.com/Neural-Systems-at-UIO/LocareJSON)), making the 3D brain atlas representation of the data available for visualisation and spatial queries.