1 Synaptome Statistics: Notes

Putative synapse locations have been detected in K15 with Forrest’s synapse detection algorithm and in W with Anish’s synapse detection algorithm. For each feature channel (Synapsin, VGlut, psd95, etc.) an 11x11x11 cube is extracted around each each putative synapse location and the voxel values are summed, creating a feature vector of length (number of channels). This gives us an \(n \times d\) matrix, where the \(n\) rows correspond to putative synapses and the \(d\) columns correspond to the summed immunoflorescence in each channel.

1.1 Clustering

We have implemented our own Hierarchical Mclust function by augmenting Mclust. In the course of exploring we used the full suite of models available in mclustModelNames p. 88

After looking through the BIC plots of each of the 11 models for each node of the tree it seemed best to use the unconstrained model “VVV” = ellipsoidal, varying volume, shape, and orientation.

1.2 MEDA Run on Z-scored data

1.2.1 1-d Heatmap

1.2.2 Location plots

1.2.3 Outliers as given by randomForest

1.2.4 Correlation Matrix

1.2.5 Cumulative Variance with Elbows

1.2.6 Paired Hex-binned plot

1.2.7 Hierarchical GMM Classifications

1.2.8 Hierarchical GMM Dendrogram

1.2.9 Stacked Cluster Means plot

1.2.10 Cluster Means

2 Cluster Synaptograms

The below table contains links to synaptograms (syn*) from each cluster as given above with a corresponding ndviz link (ndv*). The 5 synapses with feature vectors closest to their cluster mean were chosen as representatives.

C1111 C1112 C1121 C1122 C1211 C1212 C122 C21111 C21112 C2112 C212 C2211 C2212 C222
syn1_C1111 ndv1_C1111 syn1_C1112 ndv1_C1112 syn1_C1121 ndv1_C1121 syn1_C1122 ndv1_C1122 syn1_C1211 ndv1_C1211 syn1_C1212 ndv1_C1212 syn1_C122 ndv1_C122 syn1_C21111 ndv1_C21111 syn1_C21112 ndv1_C21112 syn1_C2112 ndv1_C2112 syn1_C212 ndv1_C212 syn1_C2211 ndv1_C2211 syn1_C2212 ndv1_C2212 syn1_C222 ndv1_C222
syn2_C1111 ndv2_C1111 syn2_C1112 ndv2_C1112 syn2_C1121 ndv2_C1121 syn2_C1122 ndv2_C1122 syn2_C1211 ndv2_C1211 syn2_C1212 ndv2_C1212 syn2_C122 ndv2_C122 syn2_C21111 ndv2_C21111 syn2_C21112 ndv2_C21112 syn2_C2112 ndv2_C2112 syn2_C212 ndv2_C212 syn2_C2211 ndv2_C2211 syn2_C2212 ndv2_C2212 syn2_C222 ndv2_C222
syn3_C1111 ndv3_C1111 syn3_C1112 ndv3_C1112 syn3_C1121 ndv3_C1121 syn3_C1122 ndv3_C1122 syn3_C1211 ndv3_C1211 syn3_C1212 ndv3_C1212 syn3_C122 ndv3_C122 syn3_C21111 ndv3_C21111 syn3_C21112 ndv3_C21112 syn3_C2112 ndv3_C2112 syn3_C212 ndv3_C212 syn3_C2211 ndv3_C2211 syn3_C2212 ndv3_C2212 syn3_C222 ndv3_C222
syn4_C1111 ndv4_C1111 syn4_C1112 ndv4_C1112 syn4_C1121 ndv4_C1121 syn4_C1122 ndv4_C1122 syn4_C1211 ndv4_C1211 syn4_C1212 ndv4_C1212 syn4_C122 ndv4_C122 syn4_C21111 ndv4_C21111 syn4_C21112 ndv4_C21112 syn4_C2112 ndv4_C2112 syn4_C212 ndv4_C212 syn4_C2211 ndv4_C2211 syn4_C2212 ndv4_C2212 syn4_C222 ndv4_C222
syn5_C1111 ndv5_C1111 syn5_C1112 ndv5_C1112 syn5_C1121 ndv5_C1121 syn5_C1122 ndv5_C1122 syn5_C1211 ndv5_C1211 syn5_C1212 ndv5_C1212 syn5_C122 ndv5_C122 syn5_C21111 ndv5_C21111 syn5_C21112 ndv5_C21112 syn5_C2112 ndv5_C2112 syn5_C212 ndv5_C212 syn5_C2211 ndv5_C2211 syn5_C2212 ndv5_C2212 syn5_C222 ndv5_C222

2.0.1 The following is a synaptogram from cluster C1121 @ x=770, y=6473, z=17

And as you can see, both Synapsin channels and both VGlut1 channels are “hot” which match the cluster mean as given above.