improve documentation of connections and synapses #142
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| <dt>Pre-synaptic / Post-synaptic</dt> | ||
| <dd> | ||
| Pre-synaptic refers to outputs from a neuron; post-synaptic refers to inputs to a neuron. | ||
| Post-synaptic refers to inputs to a neuron, pre-synaptic refers to outputs from a neuron. |
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I find this a bit confusing. I'm trying to think of when these terms would be used because a "post-synaptic density" refers to the region of the neuron that receives incoming signals but in lectures etc if someone says a neuron is "post-synaptic" to X, it normally means downstream of X. We could get rid of this definition and just leave the "post-synaptic sites" and "pre-synaptic sites" definitions.
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| <dt>Synapse Count</dt> | ||
| <dd>The number of synaptic connections. Higher counts indicate stronger or denser connectivity.</dd> | ||
| <dd>The number of synaptic connections. Higher counts indicate stronger or denser connectivity. neuView uses the properties from the neurons in the database.</dd> |
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I changed this to "Higher counts indicate denser connectivity." and removed the "stronger". I'm not sure if this sentence is necessarily useful, but I think it's slightly murky to say "stronger" since in the connectome we don't actually know how strong these individual connections are.
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| <dd>Presynaptic release sites where a neuron outputs signals. Also called t-bars. One presynaptic site can connect to multiple postsynaptic partners. In the neuprint data model, this is the `Neuron.pre` property.</dd> | ||
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| <dt>Connections</dt> | ||
| <dd>Input connections are conceptually similar to post-synaptic sites while a group of post-synaptic sites form a single output connection. We calculate the number of connections by identifying the connecting neurons and then use the `weight` property from the `ConnectsTo` edge between the neurons.</dd> |
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I've updated this based on our discussion before. One pre-synapse can contain multiple downstream connections.
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| <dt>Connections vs. Synapses</dt> | ||
| <dd>A single presynaptic site (t-bar) can form multiple connections to different postsynaptic partners. Therefore, the number of output connections can be greater than the number of presynaptic sites.</dd> | ||
| <dd>The numeric difference between post-synaptic sites and input connections stems from the difference in how the numbers are retrieves (see Synapse Count and Connections above). A single presynaptic site (t-bar) can form multiple connections to different postsynaptic partners. Therefore, the number of output connections can be greater than the number of presynaptic sites.</dd> |
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I thought putting this in "< blockquote >" might be useful to make it stand out a bit. I'm sure many people will be interested in this.
This is super-minor, and maybe you have ideas how to improve the wording…
I tried to give more background to the difference between the numbers in input connections and post-synpses. Without that technical background, it might be difficult to understand the difference. While we could use the same number, I think having both is actually nice for people who want to look into it in more detail…
Also, reducing the file size by a few bytes (not that this mattered…)