# Glossary

The canonical terms GuPPy uses for the entities that flow through the pipeline.

```{glossary}
store
  A single data stream — one continuous signal (e.g. a demodulated calcium
  channel) or one discrete event stream (e.g. TTL timestamps).

store_id
  The source-file identifier for a store, exactly as it appears in the
  acquisition system's files (e.g. `Dv1A` for TDT, a column name for CSV).

store_label
  The user-supplied analytic label for a store (e.g. `signal_DMS`,
  `control_DMS`, `reward`), assigned in Step 1 (Label Stores).

recording_site
  One fiber photometry recording site: a signal channel paired with its
  optional isosbestic control channel, both sharing the same label suffix. In
  a multi-fiber recording each fiber is its own recording site (e.g. `DMS`,
  `DLS`). The suffix appears in the `store_label` pair `signal_<recording_site>`
  / `control_<recording_site>` (e.g. `signal_DMS` / `control_DMS`), and in the
  preprocessed outputs `z_score_<recording_site>` / `dff_<recording_site>`. The
  suffix (`DMS`, `DLS`, …) is a free-form identifier you choose in Step 1,
  typically naming the fiber's anatomical target.

session
  One recording — a single mouse, day, and rig session. The atomic input to
  analysis.

session_folder
  The directory on disk that holds one session's raw data files.

input_root_folder
  The directory your session folders live under, chosen in the Root Folder
  Selection card. Every selected session must sit under it.

run
  One analysis pass over a session, defined by its session, its stores, its
  parameter set, and its output destination. A single session can produce many
  runs.

run_name
  The user-supplied label for a run.

run_folder
  The directory on disk holding one run's outputs, named `output_<run_name>`.

output_root_folder
  The directory the run folders are written into, chosen in the Root Folder
  Selection card. Each session's path below the {term}`input_root_folder` is
  mirrored inside it, so a session at `<input_root_folder>/subject1/session1`
  gets its run folders at `<output_root_folder>/subject1/session1/`.

group
  A named set of runs whose results are averaged together, giving a cohort- or
  animal-level view of an event's response. A group is defined in the Label
  Groups step and averaged by the Group Analysis step.

group_name
  The user-supplied label for a group (e.g. `saline`). It names the group's
  directory, `<group_name>_group`.

group_folder
  The directory on disk holding one group's definition and averaged outputs,
  named `<group_name>_group`. It behaves like a {term}`run_folder` to the steps
  that read PSTH results, so the visualizer opens it the same way.

member_run
  One {term}`run` belonging to a group. Each member contributes a single column
  to the group's averaged outputs, so the number of members is the group's
  statistical *n*.
```