Schema Chapters (User-Focused)

This section breaks the ADAMACS database into practical chapters, one per major schema. Use it as a working map when you are deciding where to read from, where to stage tasks, and which keys to carry forward.

The content here is derived from:

• live ADAMACS schema modules (adamacs_ingest/adamacs/schemas/*.py)

• dj.Diagram exports from adamacs_analysis/notebooks/21_schema_dependency_diagrams.ipynb

• DataJoint Element documentation

• reference pipeline documentation on ReadTheDocs

No personal identifiers are required to use these chapters. Work with stable keys (subject, session_id, scan_id, recording_id) and controlled vocabularies.

Read order

1. subject -> session -> scan

2. event + trial + behavior

3. imaging + model

4. mocap + virtual_markers_optitrack + pupil_tracking

5. disk for imputation workflows

• Subject Schema
• Surgery Schema
• Equipment Schema
• Session Schema
• Scan Schema
• Imaging Schema
• Model Schema
• Event Schema
• Trial Schema
• Behavior Schema
• Mocap Schema
• Virtual Markers OptiTrack Schema
• Pupil Tracking Schema
• DISK Schema

External references used

• DataJoint Elements index: https://docs.datajoint.com/elements/

• DataJoint core docs: https://docs.datajoint.com/core/datajoint-python/latest/

• Element Session: https://docs.datajoint.com/elements/element-session/latest/

• Element Calcium Imaging: https://docs.datajoint.com/elements/element-calcium-imaging/latest/

• Element DeepLabCut: https://docs.datajoint.com/elements/element-deeplabcut/latest/

• Element Event concepts: https://docs.datajoint.com/elements/element-event/0.2/concepts/

• Suite2p docs: https://suite2p.readthedocs.io/en/latest/

• Suite2p parameters: https://suite2p.readthedocs.io/en/latest/parameters/

• DeepLabCut docs: https://deeplabcut.github.io/DeepLabCut/

• DISK source: https://github.com/bozeklab/DISK

• CASCADE source: https://github.com/HelmchenLabSoftware/Cascade