Fig. 2: Performance of ACE in brain-wide segmentation of neuronal cell bodies.
a, Maximum-intensity projection rendering of whole-brain c-Fos expression, with an enlarged view of a cortical patch. Segmentation maps (blue) predicted by the ViT ensemble for the enlarged subregion are shown and compared with GT (red). b, Raw image, GT and segmentation maps for two example image patches, along with voxel-wise uncertainty maps. Regions of high uncertainty are localized around the boundary of sparsely mislabeled processes such as axons (left-hand column) and neuronal somas (right-hand column). Arrows indicate mis-segmented regions from a. c, Qualitative evaluation of segmentation accuracy of ACE versus Ilastik in terms of detection of neurons with low signal intensity or slight blurriness (top), and their shape (bottom). Arrows indicate the boundary of two neurons close to each other. d,e, Quantitative evaluation of the segmentation accuracy of ACE versus Ilastik (d), and detection accuracy of ACE versus Cellfinder (e), in terms of average DSC, precision, recall, HD95 and F1 score on test datasets (n = 12,160 unique patches with 963 ≃ 0.35 mm3) and unseen datasets (n = 1,824 unique patches of 963 ≃ 0.27 × 0.27 × 0.48 mm3). In box plots: box limits, upper and lower quartiles; center line, median; whiskers, 1.5× interquartile range; points, outliers. Mann–Whitney U-test (two-sided), ***P < 0.0001.
