ConductVision · NIH data sharing
Share ConductVision tracking data in standard formats
The ConductScience export tool packages ConductVision behavior results for sharing, with CSV tables, a data dictionary, NWB files and a validation report.
What goes into a ConductVision package
ConductVision saves
- Run records with start and end times, settings and the zone summary
- Track files with head and body positions for each frame
- Tracking engine files, one record per processed frame
- Pose files from the tests that track body parts
- The protocol and the animal list
The package holds
- Exact copies of those files, with checksums that show they are unchanged
- CSV tables for sessions, trials, positions, zones and zone visits, with a data dictionary of each column's meaning and unit
- One NWB file for each animal in each run, with its trials, positions and zone visits
- RO-Crate metadata, which describes the dataset in a form software can read
- A validation report you can open in a browser
- A draft row for the data types table in your NIH Data Management and Sharing (DMS) Plan
An example package
The export tool built this package from synthetic open field results for three mice, saved in ConductVision's own file formats.
- Original files
- 10
- Tables
- 14
- Columns with a definition
- 158 of 161
- NWB files
- 3
| Table | Rows | Columns with a definition |
|---|---|---|
| Sessions | 3 | 19 of 19 |
| Protocols | 1 | 8 of 8 |
| Protocol settings | 23 | 6 of 6 |
| Animal list | 3 | 8 of 8 |
| Trials | 3 | 14 of 14 |
| Track positions | 13,500 | 27 of 27 |
| Zone summary | 27 | 12 of 12 |
| Zone grid | 27 | 10 of 10 |
| Zone visits | 469 | 12 of 12 |
| Tracking engine files | 3 | 13 of 13 |
| Tracking engine frames | 13,500 | 18 of 18 |
| Open | 3 | 3 of 4 |
| Open | 3 | 3 of 5 |
| NWB files | 3 | 5 of 5 |
In the preview below, the unit under each column name comes from the package's data dictionary. Columns of names, IDs or yes-or-no values have no unit.
| subject | zone | entries count | duration_s s | time_fraction fraction (0 to 1) | distance_cm cm |
|---|---|---|---|---|---|
| M01 | O11 | 21 | 43.0 | 0.15 | 295.78 |
| M01 | O12 | 15 | 31.0 | 0.1 | 208.69 |
| M01 | O13 | 9 | 24.0 | 0.08 | 166.71 |
| M01 | O21 | 36 | 59.0 | 0.2 | 392.08 |
| M01 | O22 | 31 | 35.0 | 0.12 | 241.22 |
| M01 | O23 | 10 | 24.0 | 0.08 | 167.93 |
| M01 | O31 | 20 | 57.0 | 0.19 | 389.2 |
| M01 | O32 | 19 | 23.0 | 0.08 | 168.1 |
| M01 | O33 | 0 | 0.0 | 0.0 | 0.0 |
Draft data types row for this example
Behavior tracking results from ConductVision Behavior (OpenField): session, trial and protocol tables with documented columns, track positions and zone visits with documented columns, other run records and files as CSV tables, NWB files of positions and zone visits for each run and animal and the 10 original files. Species: Mus musculus.
Your lab edits the draft and names the repository that will hold the data, then adds both to the plan's data types table.
Checks on the example package
All of the tool's required checks passed. Two checks (column definitions and NWB files) also made suggestions, listed below the table.
| Check | Result | What the check found |
|---|---|---|
| Reading the files | Passed | The tool read 10 files from the result folder. |
| Required files | Passed | The package has its README, plan draft, RO-Crate metadata, checksum list, data dictionary and validation report. |
| Checksums | Passed | Every file matches its SHA-256 checksum in the checksum list. The tool wrote the list last and ran this check before moving the package into its folder. |
| Original files | Passed | Each of the 10 copies has the same SHA-256 checksum as its original, and no original changed during copying. |
| Metadata | Passed | Every required detail is filled in, either from the files or by the lab. |
| RO-Crate | Passed | The RO-Crate metadata meets every required rule of the RO-Crate 1.3 profile. Checked with the RO-Crate validator |
| Tables | Passed | All 14 tables match the column names and value types in the data dictionary. Checked with the Frictionless validator |
| Column definitions | Suggestions | 158 of 161 columns have a written meaning, with a unit where one applies. The other 3 are listed below. |
| NWB files | Suggestions | The tool reopened all 3 NWB files, and every value matched the tables. Checked with PyNWB, the ndx-pose extension and NWB Inspector |
| OME-TIFF files | Not applicable | This package has no OME-TIFF files. |
| Data dictionary | Passed | The data dictionary lists every column, including any still without a written meaning. |
Columns without a definition
| Table | Columns |
|---|---|
| Open | Activities |
| Open | RearingThreshold, RearingInterval |
Add their definitions to your deposit's README, or ask us to add them to the export tool.
NWB Inspector suggestions
| Suggestion | Files |
|---|---|
| Description is missing. | 3 |
| Experimenter is missing. | 3 |
| Metadata /general/institution is missing. | 3 |
| This table has only a single row; it may be better represented by another data type. | 3 |
These are NWB Inspector's best-practice suggestions, not errors. The NWB files still open and match the tables.
What you fill in
Your lab adds the details below, and the tool reads everything else from your files. The validation report names any detail still missing.
Dataset
A title, a short description, and a license or access statement.
People
At least one creator, with an ORCID iD and affiliation if you have them.
Human data
Whether any of the data come from human participants.
Subjects
Species, strain, sex and age, given once for all animals or separately for each. Write age like P90D for 90 days (an ISO 8601 duration).
Recording
The time zone of the recording computer, and the video frame rate if the files do not state it.
Calibration
Pixels per centimeter, if the files do not state it. Each NWB file uses it to convert positions to centimeters.
What your lab is responsible for
The export tool only prepares and checks the files.
Your lab writes the DMS Plan and carries out the approved version. Your lab also chooses the repository and handles consent, privacy and who may access the data.
Questions
- Which ConductVision tests get NWB files?
- Every test's results become tables. Tests that also save ConductVision's standard track file, such as open field, get one NWB file for each animal in each run.
- Does the package include pose data?
- Yes. The tracking engine's pose files become a table. If the video frame rate is known, they also go into the NWB files.
- Does ConductVision need changes to work with the tool?
- No. The tool reads the folders ConductVision already saves, so nothing changes in how your lab runs it.
Request the export tool
Tell us what you plan to share. We will reply with the tool and how to set it up.
