Data Pipeline

Element ZStack is composed of two main schemas, volume and bossdb. Data export to BossDB is handled with the bossdb schema and upload utilities.

• volume module - performs segmentation of volumetric microscopic images with cellpose.

• bossdb module - uploads data to BossDB, creates a Neuroglancer visualization, and stores the relevant URLs.

Each node in the following diagram represents the analysis code in the pipeline and the corresponding table in the database. Within the workflow, Element ZStack connects to upstream Elements including Lab, Animal, Session, and Calcium Imaging. For more detailed documentation on each table, see the API docs for the respective schemas.

reference schema (API docs)

Table	Description
Device	Lab equipment metadata

subject schema (API docs)

• Although not required, most choose to connect the Session table to a Subject table.

Table	Description
Subject	Basic information of the research subject

session schema (API docs)

Table	Description
Session	Unique experimental session identifier

scan schema (API docs)

Table	Description
Scan	A set of imaging scans performed in a single session

volume schema (API docs)

Table	Description
Volume	Details about the volumetric microscopic images
VoxelSize	Voxel size information about a volume in millimeters
SegmentationParamSet	Parameters required for segmentation of the volumetric scans
SegmentationTask	Task defined by a combination of Volume and SegmentationParamSet
Segmentation	The core table that executes a SegmentationTask
Segmentation.Mask	Details of the masks identified from the segmentation

bossdb schema (API docs)

Table	Description
VolumeUploadTask	Names of the collection, experiment, and channel where data will be uploaded to BossDB
VolumeUpload	Uploads image and segmentation data to BossDB
VolumeUpload.WebAddress	Stores the BossDB and Neuroglancer URLs for each upload