synapse.py

import marshmallow as mm
from emannotationschemas.schemas.base import (
    AnnotationSchema,
    BoundSpatialPoint,
    SpatialPoint,
    ReferenceAnnotation,
)


class BaseSynapseSchema(AnnotationSchema):
    pre_pt = mm.fields.Nested(
        BoundSpatialPoint,
        required=True,
        description="a nearby point located in the presynaptic compartment of the synapse",
        order=0,
    )
    post_pt = mm.fields.Nested(
        BoundSpatialPoint,
        required=True,
        description="a nearby point located in the postsynaptic compartment of the synapse",
        order=2,
    )

    @mm.post_load
    def check_root_id(self, data, **kwargs):
        pre_id = data["pre_pt"].get("root_id", None)
        post_id = data["post_pt"].get("root_id", None)
        # when the root_id is present
        # we should set the valid flag depending up on this rule
        # when the root_id is not present
        # (i.e. when posting new annotations with no root_id's in mind)
        # then the valid flag should be not present
        if pre_id is not None:
            data["valid"] = False if pre_id == post_id else True
        else:
            data.pop("valid", None)
        return data


class NoCleftSynapse(BaseSynapseSchema):
    score = mm.fields.Float(
        description="synapse score (see table metadata for description of score)"
    )


class SynapseSchema(BaseSynapseSchema):
    ctr_pt = mm.fields.Nested(
        SpatialPoint, required=True, description="central point", order=1
    )
    size = mm.fields.Float(description="size of synapse")


class NoCenterSynapse(BaseSynapseSchema):
    size = mm.fields.Float(description="size of synapse")


class BuhmannSynapseSchema(BaseSynapseSchema):
    connection_score = mm.fields.Float(
        description="score assigned by Buhmann et al. 2019"
    )
    cleft_score = mm.fields.Float(
        description="score derived by Buhmann et al. 2019 "
        "by combining their synapses with the synapse "
        "segmentation from Heinrich et al. 2018"
    )


class BuhmannEcksteinSynapseSchema(BuhmannSynapseSchema):
    gaba = mm.fields.Float(description="Gaba probability by Eckstein et al. 2020")
    ach = mm.fields.Float(
        description="Acetylcholine probability by Eckstein et al. 2020"
    )
    glut = mm.fields.Float(description="Glutamate probability by Eckstein et al. 2020")
    oct = mm.fields.Float(description="Octopamine probability by Eckstein et al. 2020")
    ser = mm.fields.Float(description="Serotonin probability by Eckstein et al. 2020")
    da = mm.fields.Float(description="Dopamine probability by Eckstein et al. 2020")
    valid_nt = mm.fields.Bool(
        description="False = no neurotransmitter prediction available."
    )


class PlasticSynapse(SynapseSchema):
    plasticity = mm.fields.Int(
        required=True,
        validate=mm.validate.OneOf([0, 1, 2, 3, 4]),
        description="plasticity state 0:not synapse 1:normal 2:mild 3:strong 4:not rated",
    )


class ValidSynapse(ReferenceAnnotation):
    is_valid = mm.fields.Bool(
        required=True,
        description="Valid annotation for synapses",
    )