Figure 8.

Whole brain nuclei detection and assignment to anatomical labels. (A) Automated verification within the depicted sub-ROI shows truth blobs as small, opaque dots and detections as larger, translucent circles. Blue dots are correctly detected truth blobs, while purple dots are misses. Green circles are correct detections, and red circles are false. Correct detections and corresponding truth blobs may be separated by up to a few z-planes if the detector correctly identified a nucleus but slightly off its center in the z-axis. The interface allows inspection to determine where the detector may have worked or failed to guide further optimization. (B) A receiver operating characteristic (ROC) curve from a Grid Search test of several combinations of detection setting parameters with more ROIs of larger size. The minimum and maximum object size parameters and an isotropic scaling factor were varied, with the false discovery rate (FDR, x-axis) and sensitivity (y-axis) shown for each combination. The point labels show the isotropic factor (1 = isotropic, 0.5 = z-scale is half that of x and y), and the color and point symbol correspond to the legend values denoting min/max size parameters. (C) Example of automated verifications in one of these larger ROIs. A sub-image (red arrow) was extracted from the original whole-brain image and 10 ROIs annotated as ground truth, and a wide layout was selected (green arrow). (D) Density heat map of nuclei detected across a full-resolution sample brain using the pipelines script. (E) High resolution serial 2D plots from the ROI Editor show the individual detected nuclei. The ROI coordinates were found by specifying a region ID (below the green arrow in part C), Allen ID 16382 (the alar thalamus, showing the left side), which positioned the ROI to the center of this label. Overview plots show the ROI in context with anatomical labels overlaid and the left alar thalamus highlighted in light gold.