Extended Data Fig. 5: Comparing BANKSY and non-spatial clustering results on the VeraFISH data to SpiceMix (HMRF), SpaGCN and FICT (HMRF).

Similar to Extended Data Fig. 4. As before, the number of clusters was varied by adjusting parameters related to clustering resolution. Each column represents one clustering run for the indicated method at a given resolution (controlled by the number of clusters input parameter, N). Blue arrows indicate the runs compared in Fig. 4. Green and red boxes indicate success and failure (respectively) to identify the known neuronal or oligodendrocyte subclusters (Fig. 4; Supplementary Fig. 18). SpiceMix correctly separated the thalamic and fornix oligodendrocytes, merged the somatosensory cortex neurons with either the CA3 neuron (orange clusters) or the dentate gyrus neurons (brown and light green clusters). SpaGCN was able to identify the CA3 neurons, but merged the somatosensory cortex neurons with cells in the dentate gyrus (brown cluster), and was unable to separate the thalamic and fornix oligodendrocytes (red boxed green clusters). FICT, like Giotto in Extended Data Fig. 4, tended to group cells into disconnected spatial patches that do not conform to known anatomical structures (dashed red boxes), and tended to merge the dentate gyrus, CA1, CA3 and somatosensory cortex neurons into one or two clusters (light and dark blue clusters).