We’ve been successfully using the connectivity data provided at the NMC portal for constructing neural networks of our own. After going through the paper and looking hard at the data, we however haven’t been able to answer some questions regarding differences between the paper and the data at the NMC portal (https://bbp.epfl.ch/nmc-portal/documents/10184/7288948/pathways_anatomy_factsheets_simplified.json). Specifically:
Issue 1: In the paper for the total number of synapses in the microcircuit, you provide the estimate ~37 synapses (36.7 ± 4.2 million synapses). However if you take the sum of total_synapse_count 's, you get a number close to 60 million (59 245 093).
Issue 2: When plotting the connection_probability variable as a heatmap similarly to Figure 7B in the paper, two spots stand out: L4_BTC:L4_ChC with 40% probability and L4_NGC:L4_ChC with 100% probability. These spots are blank in the paper. Why have they been weeded out from Fig 7B but left in the json data?
Issue 3: There are also some connections in Figure 7B that don’t have a connection_probability set in the json data, eg. L6_NGC:L6_SBC. Why are they missing from the json data?
We’d be really happy if someone took the time to clarify these issues for us.
PhD student, Univ.of Helsinki