add synapse_with_neuron schema

[jinhan]

Adding SynapseWithNeuron class that inherits SynapseSchema.
In SynapseWithNeuron, pre_neuron_pt is a point of the sample voxel of the neuron where the presynaptic compartment of the synapse is located. post_neuron_pt is for the postsynaptic compartment.

[fcollman]

It seems you just want to use this schema.. https://github.com/CAVEconnectome/EMAnnotationSchemas/blob/master/emannotationschemas/schemas/synapse.py#L10

I think you should just add this to the advertised set of schemas.. you have made subtle changes to the column names which don't follow the conventions of other synapse schemas.

[jinhan]

I would like to add each of the pre_neuron_pt and post_neuron_pt while keeping the synapse schema. Could you explain more about how to add to the advertised set of schemas?

[fcollman]

from the README of the repo:

Import this schema into init.py, and add the schema to the type_mapping dictionary, giving it a string based key. This will be the annotation_type of your new class of annotation.

you didn't add this to the dictionary.. this is how you go from string>python class.

I'm suggesting that you import the already existing BaseSynapseSchema with 'pre_pt' and 'post_pt' so this schema matches all the other synapse schemas, rather than pre_pt_neuron and post_pt_neuron. This will just make the column names longer 'pre_pt_neuron_root_id' and 'post_pt_neuron_root_id' which is kind of a lot to type and not really that much clearer. Plus you can have synapses not onto neurons (i.e. OPC and astrocyte) so its not good from a biology point of view.

[jinhan]

I added the schema name to the dictionary.

I'm sorry that my goal for this new schema is unclear. I want to use both pre_pt and pre_neuron_pt in the same schema. So I need to add other columns for neuron ids even though I inherit BaseSynapseSchema. This image shows the schema that I expected.

I agree that neuron is inappropriate term regarding generalization.

[fcollman]

in what context would a user use pre_pt and pre_neuron_pt (or post/post_neuron_pt) .. why are they both bound spatial points?

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On Mon, Apr 8, 2024 at 1:12 PM Jinhan Choi ***@***.***> wrote: I added the schema name to the dictionary. I'm sorry that my goal for this new schema is unclear. I want to use both pre_pt and pre_neuron_pt in the same schema. So I need to add other columns for neuron ids even though I inherit BaseSynapseSchema. This image shows the schema that I expected. Screenshot.2024-04-08.at.16.02.58.png (view on web) <https://github.com/CAVEconnectome/EMAnnotationSchemas/assets/3071179/2a13b7c3-eb50-486d-b0af-8cfe837f5093> I agree that neuron is inappropriate term regarding generalization. — Reply to this email directly, view it on GitHub <#84 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAF7ABIYGK6UV73FCMILOKDY4L237AVCNFSM6AAAAABF47YXAWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBTGU3DAMZRGY> . You are receiving this because you commented.Message ID: ***@***.***>

[jinhan]

I think neuron_pts may only be needed for our synapses table. As you know, I try to utilize pre/post neuron id in our dataset to solve the problem of some synapses and segments not being linked. And I thought that BoundSpatialPoints was the way to get supervoxe_id and root_id.
If this is a case specific to our dataset, should I just use it in my repository rather than push it to this repository?