Combine a session split across two data files#

Some acquisition systems split one continuous recording into two separate session folders — for example a system that writes a new file when a recording is paused and resumed, or splits a long session at a fixed size limit. Combine Data? stitches the matching channels from both halves back into a single continuous trace before preprocessing. This is an unusual case — if your sessions are already one file each, skip this guide.

Before you start#

Each half needs its own session folder. The recording sites in both folders must be labeled identically in Step 1: Label Stores — the same signal_<site> / control_<site> pair names on both halves — otherwise combining fails with a message telling you to re-run Step 1.

Naming your session folders#

GuPPy decides which half comes first, and where the combined result is written, by sorting the two session folders’ paths alphabetically — not by recording time. Name your folders so alphabetical order matches recording order (for example Session_part1 / Session_part2, or a date-time prefix). If the names sort the wrong way, the halves are spliced in the wrong order with no error.

The combined result is written into whichever folder sorts first, overwriting its Step 3 outputs. The other folder’s outputs are left untouched.

Matching the two halves#

GuPPy groups sessions to combine by their run name — the suffix on the output_<run name> directory Step 1 creates — not by session name. Both halves must use the same run name.

  1. Run Step 1: Label Stores on the first half, labeling its recording sites as usual. Leave Run name at the 1 GuPPy fills in (or set an explicit name if you prefer — the second half just needs to match it).

    The Label Stores GUI's "Choose where to save these store labels" section, with Create new run selected and the Run name field holding the default 1

  2. Run Step 1: Label Stores on the second half, using the same recording-site labels and the same run name as the first.

  3. Back on the homepage, select both session folders together in Input Folder Selection.

    The Input Folder Selection file browser with both session folders, Photo_048_392-200728-121222 and Photo_63_207-181030-103332, moved into the Selected files list

  4. Open Output Folder Selection and, in Existing runs (steps 2–5), pick each session’s matching output run (e.g. both output_1).

  5. In the Input Folder Selection card, set Combine Data? to True (below the file browser, where it qualifies the sessions you just picked).

Running the pipeline#

Run Step 2: Read Raw Data, then Step 3: Preprocess. Combining happens automatically inside Step 3, right after per-session timestamp correction, and writes the merged result into the first (alphabetically) session’s output folder — see Naming your session folders above.

Continue to Step 4: PSTH Computation and Step 5: Visualization with Combine Data? still True. Both already know to read from the merged run instead of treating the two sessions separately.

What lands on disk#

Combining adds one file to the destination run folder:

File

Contents

combine_storesList.csv

Merged store mapping, union of both sessions’ storesList.csv

The combined traces themselves overwrite that folder’s timeCorrection_<site>.hdf5, <store_label>.hdf5, and <event>_<site>.hdf5 files. See Output data model for the full file layout.

Notes#

  • Both files being combined must share the same sampling rate; GuPPy raises an error naming the mismatched files if they don’t.

  • Combining is re-runnable. Re-running Step 3 with Combine Data? on recomputes the merge from the raw, per-session data each time, so repeated runs don’t compound.