Glossary#

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

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 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 run_folder to the steps that read PSTH results, so the visualizer opens it the same way.
member_run#: One 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.