Metrics structuring for contribution

Note

Prerequisites

This article requires that you understand how data is stored on SynDB, we recommend reading through the overview article if you are uncertain.

This article is a guide for contributors who wish to upload their data to SynDB. Please don’t hesitate to ask for help on the Discord channel if you have any questions; this part can be challenging.

Each SynDB table has its own expected columns and types. The current CLI and ETL importers are the authoritative validators: structure your data so it passes syndb data validate for direct uploads, or the relevant syndb etl <dataset> validate command for a supported importer.

The column names and the values stored under them must match the current importer schema for the table you are contributing to. Use the glossary at the end of this article as a quick reference, then validate early with the current tooling before preparing a full upload.

Note

Nano

We use nanometers as the unit for all measurements; includes volume, radius, and distance.

Supporting source assets

SynDB expects your primary contribution to be tabular, analysis-ready data. You may also attach supporting source assets such as meshes or SWC skeletons. This does not refer to raw imaging volumes. Place the absolute path to the file in your table file. The following are supported:

Meshes in .glb format, column name: mesh_path
SWC files, .swc, column name: swc_path

This list is the main tracker for the supported formats. You may request additional formats on the Discord channel. The SynDB team will review the request and consider adding the new format to the platform.

Columns

Most column types are self-explanatory, but some require additional explanation.

Identifiers and relations

The CID column defined in your table can have any unique hashable value, it will be replaced by a UUID when uploaded to SynDB. When uploading a relational dataset, the cid column in the parent will be used to correlate the relations to the children by their parent_id; meaning the hashable value in the parent cid column must match the parent_id in the child. parent_enum can be omitted as the compartments are defined at the tabular level, and will, therefore, be added automatically.

Example

Notice the parent_id column in the child table, this is the cid of the parent table. The parent_enum column is not present in the child table, as it is defined at the tabular file name.

vesicle.csv, child

cid	neurotransmitter	voxel_radius	distance_to_active_zone	minimum_normal_length	parent_id	centroid_z	centroid_x	centroid_y
0	glutamate	26.9129	705.2450	23	1	4505.232	1996.224	4953.6
1	glutamate	25.5388	615.0213	23	1	4505.232	1996.224	4953.6
2	glutamate	29.5260	513.0701	23	1	4505.232	1996.224	4953.6
3	glutamate	30.5131	479.9224	23	1	4505.232	1996.224	4953.6
4	glutamate	28.3977	454.8248	23	1	4505.232	1996.224	4953.6
5	glutamate	30.2033	459.7557	23	2	4505.232	1996.224	4953.6
6	glutamate	33.4548	374.8131	23	2	4505.232	1996.224	4953.6
7	glutamate	32.0890	455.9293	23	4	4505.232	1996.224	4953.6

axon.csv, parent

voxel_volume	mitochondria_count	total_mitochondria_volume	cid
385668034.56	1	93208043.52	1
1492089016.32	4	412054179.84	2
327740497.92	0	0	4

Glossary

Key	Description
`dataset_id`	The unique identifier for the dataset, of type `uuid`.
`cid`	The unique identifier for a SynDB unit within the dataset, of type `uuid`.
`parent_id`	The CID of the parent component, of type `uuid`.
`parent_enum`	An integer representing the type or category of the parent component, of type `int`.
`polarity`	The polarity of the neuron, of type `ascii`.
`voxel_volume`	The volume of the voxel, of type `double`.
`voxel_radius`	The radius of the voxel, of type `double`.
`s3_mesh_location`	The location of the mesh in S3 storage, of type `smallint`.
`mesh_volume`	The volume of the mesh, of type `double`.
`mesh_surface_area`	The surface area of the mesh, of type `double`.
`mesh_area_volume_ratio`	The ratio of the surface area to the volume of the mesh, of type `double`.
`mesh_sphericity`	The sphericity of the mesh, of type `double`.
`centroid_z`	The z-coordinate of the centroid, of type `double`.
`centroid_x`	The x-coordinate of the centroid, of type `double`.
`centroid_y`	The y-coordinate of the centroid, of type `double`.
`s3_swb_location`	The location of the SWB in S3 storage, of type `smallint`.
`terminal_count`	The count of terminals, of type `int`.
`mitochondria_count`	The count of mitochondria, of type `int`.
`total_mitochondria_volume`	The total volume of mitochondria, of type `double`.
`neuron_id`	The unique identifier for the associated neuron, of type `uuid`.
`vesicle_count`	The count of vesicles, of type `int`.
`total_vesicle_volume`	The total volume of vesicles, of type `double`.
`forms_synapse_with`	The unique identifier of the synapse that the component forms with, of type `uuid`.
`connection_score`	The score representing the strength or quality of the connection, of type `double`.
`cleft_score`	The score for the synaptic cleft, of type `int`.
`GABA`	The concentration or presence of GABA neurotransmitter, of type `double`.
`acetylcholine`	The concentration or presence of acetylcholine neurotransmitter, of type `double`.
`glutamate`	The concentration or presence of glutamate neurotransmitter, of type `double`.
`octopamine`	The concentration or presence of octopamine neurotransmitter, of type `double`.
`serine`	The concentration or presence of serine neurotransmitter, of type `double`.
`dopamine`	The concentration or presence of dopamine neurotransmitter, of type `double`.
`root_id`	The external root identifier from the source platform (e.g. FlyWire), of type `int`.
`pre_id`	The unique identifier of the pre-synaptic component, of type `uuid`.
`post_id`	The unique identifier of the post-synaptic component, of type `uuid`.
`dendritic_spine_count`	The count of dendritic spines, of type `int`.
`neurotransmitter`	The type of neurotransmitter present in a vesicle, of type `ascii`.
`distance_to_active_zone`	The distance from the vesicle to the active zone, of type `double`.
`minimum_normal_length`	The minimum normal length, of type `int`.
`ribosome_count`	The count of ribosomes within the endoplasmic reticulum, of type `int`.

Synapse DB