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@@ -1,3 +1,93 @@
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-# Ronny_Bergmann_AirtrackMotorPlanning_RawData
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+# Raw data for: Bergmann, Sehara _et al._, 2022
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-The raw-data repository for the project "AirtrackMotorPlanning" (examines whether whiskers and pupil positions predict the animal's motor plans)
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+The raw-data repository for the project "AirtrackMotorPlanning" (examines whether whiskers and pupil positions predict the animal's motor plans)
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+
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+
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+
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+### Contents
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+
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+- [File organization](#file-organization)
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+- [Acquisition](#acquisition)
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+- [Behavioral state annotation](#behavioral-state-annotation)
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+
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+
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+
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+## File organization
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+
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+### File names
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+
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+The files are organized as: `<ANIMAL>/<SESSION>/<DOMAIN>/<ANIMAL>_<SESSION>_<DOMAIN>_run<TRIAL>`, where:
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+
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+- `ANIMAL` representing the ID of the animal (in the pattern `MLAxxxxxx`).
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+- `SESSION` being the name of the session (in the pattern `sessionYYYY-MM-DD-001`).
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+- `DOMAIN` representing the domain of recording (see below).
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+- `TRIAL` being the trial index during the session.
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+
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+### Domain names
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+
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+| Domain name | Description |
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+| ----------- | ------------------------------------------------------------ |
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+| top | AVI files taken at 200 Hz using ZR View (a custom video acquisition software) under the near-UV lighting, trial-based. See [acquisition](#acquisition) for more details. |
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+| states | CSV files containing manual annotation of behavioral states based on the top-view videos, trial-based. See [behavioral state annotation](#behavioral-state-annotation) for more details. |
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+| left-eye | AVI files of left eye videos taken at 100 Hz using PylonPD (a custom video acquisition software) under the IR-lighting, trial-based. |
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+| right-eye | AVI files of right eye videos taken at 100 Hz using PylonPD (a custom video acquisition software) under the IR-lighting, trial-based. |
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+
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+
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+
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+## Acquisition
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+
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+Below is the schematics of acquisition. The "Start/Stop" signal from the Arduino Mega controls the timings of the beginning and the end of acquisition for each domain.
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+
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+
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+
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+
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+
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+
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+
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+## Behavioral state annotation
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+
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+### Names of states
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+
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+Basically the idea is to take notes of the period of frames when the subject does a particular action:
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+
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+1. Standing still
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+ - at the end of a corridor
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+ - before starting another trial (`AtEnd`)
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+ - waiting for the lick port to come (`Expect`)
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+ - at the junction between a corridor and the central arena (`AtCenter`)
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+ - in the midway in a corridor (`AtMidpoint`)
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+2. Moving backward in a corridor (`Backward`)
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+3. Moving forward in a corridor (`Forward`)
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+4. Turning in the central arena
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+ - in the left (`Left`)
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+ - in the right (`Right`)
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+5. Licking from the lick port (`Lick`)
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+
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+### Criteria of transition
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+
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+Transitions from `Backward` to `Left`, or vice versa, would be one of the the most difficult decisions. Sina used the level of the subject's eyes as the reference point, and considered "in the lane (i.e. `Backward` or `Forward`) if their eyes are still in the corridor.
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+
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+Another difficulty is determining on when the animal starts to move. You will have to decide case-by-case in accordance with e.g. consistency of motion and positions.
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+
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+### Format
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+
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+You can keep it as a CSV file, consisting of entries like below:
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+
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+| Trial | FromFrame | ToFrame | State | notes |
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+| ----- | --------- | ------- | -------- | ---------------------- |
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+| 1 | 1 | 4036 | AtEnd | |
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+| 1 | 4037 | 4385 | Backward | |
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+| 1 | 4386 | 4473 | Right | (ambiguous transition) |
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+| 1 | 4480 | 4702 | Forward | |
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+| ... | ... | ... | ... | ... |
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+
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+1. You can enter multiple trials in one file, if you want.
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+ It is better to have a column holding the trial numbers, in any case.
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+2. Frames start from one. This is in accordance with how ZR View works.
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+3. Frames must contain the start (inclusive) and the stop (inclusive) indexes.
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+ This is because it is sometimes hard to determine the transitions, and you
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+ may want to skip some ambiguous frames for annotation.
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+
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+----
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+
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+Copyright (c) 2022, Ronny Bergmann, [Keisuke Sehara](https://orcid.org/0000-0003-4368-8143), Sina E. Dominiak, [Julien Colomb](https://orcid.org/0000-0002-3127-5520), [Jens Kremkow](https://orcid.org/0000-0001-7077-4528), [Matthew E. Larkum](https://orcid.org/0000-0001-9799-2656), [Robert N. S. Sachdev](https://orcid.org/0000-0002-6627-0199), [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)
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