---
license: cc-by-4.0
pretty_name: ca1-online-decoding task data
tags:
  - neuroscience
  - calcium-imaging
  - two-photon
  - hippocampus
  - place-cells
  - terminal-bench-science
---

# ca1-online-decoding

Data for the terminal-bench-science task `ca1-online-decoding`: decode a mouse's position in an
open field from a stream of raw two-photon calcium imaging of hippocampal CA1, one frame at a time.
This card is the only place the provenance is written down; the task deliberately gives the agent
no acquisition metadata beyond the frame rate, the pixel scales and the plane alternation stated in
its instruction.

## Source

Zong, W., Obenhaus, H. A., Skytoen, E. R., et al. (2022). Large-scale two-photon calcium imaging in
freely moving mice. Cell 185(6), 1240-1256. Deposited in the NIRD Research Data Archive,
DOI 10.11582/2022.00008, licence CC BY 4.0. One session of one mouse imaged in CA1 with the MINI2P
miniature two-photon microscope while foraging in a square open field: mouse 97289, session
2021-03-22, the deposit's `ca1-97289` tarball, ScanImage TIFFs `97289-20210322_00001.tif` to
`_00003.tif` (8700 pages each) and their DeepLabCut tracking files.

## What was done

The three TIFFs were read in order (26,100 pages, int16, 256 x 256, the focus alternating between
two planes 50 micrometres apart on every page at 14.49 frames per second) and split in time only,
at page 13,050, into `input/` (the agent's training segment) and `verification/` (the held-out
segment the verifier streams to the agent's program and grades on). Pages are written as acquired,
interleaved and unregistered, to a plain BigTIFF without the ScanImage headers. `tracking.csv` in
each folder is the DeepLabCut output for the same pages, one row per page, the file's three header
rows kept, the index column restarted at 0. Nothing else was changed. The task's
`authoring/provenance/build_data.py` is the exact script.

| file | pages / rows | sha256 |
|---|---|---|
| `ca1-online-decoding/input/frames.tif` | 13050 | 43a65fc72f910fbe8d2e1bc498b6b464f7fa241afd26497460c46c92c0082662 |
| `ca1-online-decoding/input/tracking.csv` | 13050 | 8ca8f8753fc9687398e69cface8a8687813247b6f547304bbe0f34b9240bac27 |
| `ca1-online-decoding/verification/frames.tif` | 13050 | 687bf07ec619e3234d2450bdac21d420245fa9b429ccd747e358dd1cbec2b12a |
| `ca1-online-decoding/verification/tracking.csv` | 13050 | da9a5e8c5cf0a74d4b02c682b558b640ef0e91ba1f38b846c6a5372b3c12a122 |

The camera scale, 0.08 cm per pixel, is `TrackingResolution` in the deposit's
`ExperimentInformation.mat`; the imaging scale is 0.96 micrometres per pixel.

The `input/` files are pulled into the agent's environment image and the `verification/` files
into the verifier image only, each at a pinned commit of this repository and checked against the
hashes above at build time.