SI Appendix To accompany “ Clique topology reveals intrinsic geometric structure in neural correlations . ”

Selection criteria for cells and recordings. During each of the three behavioral conditions (spatial navigation, wheel running, and REM sleep), only putative pyramidal cells whose average firing rates were in the 0.2-7 Hz range were used. Putative interneurons, defined as having an average firing rate above 7 Hz over an entire recording session, were excluded. Recordings with at least N=60 neurons satisfying these criteria were selected for the analyses. A total of 18 recordings from 5 animals met the selection criteria. These consisted of 9 “open field” spatial navigation data sets from three animals, 5 wheel running data sets from two animals, and 4 REM sleep data sets from two animals. Periods of REM sleep were detected from the local field potential using the ratio of total delta power (0.1-3 Hz) to total theta power (5-10 Hz) in the spectrogram of the EEG. Periods with delta/theta ratio less than 1 were considered REM sleep. The number of cells and length of each recording were: N = 76 (16 min), N=81 (16 min), N=72 (63 min), N=88 (63 min), N=68 (59 min), N=64 (50 min), N=67 (50 min), N=74 (59 min), and N=66 (60 min) for spatial navigation; N=77 (26 runs, 6 min), N=73 (25 runs, 5 min), N=83 (13 runs, 5 min), N=67 (7 runs, 2 min), and N=64 (10 runs, 3 min) for wheel running; and N=67 (30 s), N=69 (4 min), N=60 (2.5 min), and N=61 (3.5 min) for REM sleep. The N=88 spatial navigation data set was used in Figure 3.