Biotracks: a standard format for cell migration-derived tracking files
Biotracks provides a standard format for cell migration tracking files and a series of converters from popular tracking sofware packages to the biotracks format, which is a specialization of the Frictionless Tabular Data Package .
Installation from sources (Python 3 only)
python setup.py install
Installation from PiPy
pip install biotracks
Usage
Move to the scripts directory and run:
python create_dpkg.py your_tracking_fileThis will create a tabular data package directory containing:
- a csv file for the objects (e.g., cells)
- a csv file for the links (linear collections of objects)
- the json descriptor file for the data package
The latter will look like this:
{
"name": "cmso_tracks",
"resources": [
{
"name": "cmso_objects_table",
"path": "objects.csv",
"schema": {
"fields": [
{
"constraints": {
"unique": true
},
"description": "",
"format": "default",
"name": "cmso_object_id",
"title": "",
"type": "integer"
},
{
"description": "",
"format": "default",
"name": "cmso_frame_id",
"title": "",
"type": "integer"
},
{
"description": "",
"format": "default",
"name": "cmso_x_coord",
"title": "",
"type": "number"
},
{
"description": "",
"format": "default",
"name": "cmso_y_coord",
"title": "",
"type": "number"
}
],
"primaryKey": "cmso_object_id"
}
},
{
"name": "cmso_links_table",
"path": "links.csv",
"schema": {
"fields": [
{
"description": "",
"format": "default",
"name": "cmso_link_id",
"title": "",
"type": "integer"
},
{
"description": "",
"format": "default",
"name": "cmso_object_id",
"title": "",
"type": "integer"
}
],
"foreignKeys": [
{
"fields": "cmso_object_id",
"reference": {
"datapackage": "",
"fields": "cmso_object_id",
"resource": "cmso_objects_table"
}
}
]
}
}
]
}Configuration
Some formats require a configuration file that specifies how to map object IDs, coordinate names, etc. This file must be in the INI format with two sections:
- TOP_LEVEL_INFO: specifies a name for the data package and additional (optional) information
- TRACKING_DATA: specifies how to map information from the source format to the biotracks column headers
You can provide a configuration file by passing it via the -c option to create_dpkg.py; if this option is not set, the script will look for a biotracks.ini file in the same directory as your tracking file; if this is not found, the script will use default names for both the overall package and the column headers.
Example:
[TOP_LEVEL_INFO] author = the author of the dp title = a title describing the dp name = a name for the dp author_institute = the insitute of the author author_email = a valid email address [TRACKING_DATA] cmso_x_coord = the column name pointing to the x coordinate cmso_y_coord = the column name pointing to the y coordinate cmso_z_coord = the column name pointing to the z coordinate cmso_frame_id = the column name pointing to the frame information cmso_object_id = the object identifier cmso_link_id = the link identifier Examples -------- `CELLMIA <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/CELLMIA>`_ . `CellProfiler <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/CellProfiler>`_ . `ICY <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/ICY>`_ . `Mosaic <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/Mosaic>`_ . `TrackMate <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/TrackMate>`_ .
Releases
- Latest release - Biotracks 0.5.0:
- Other releases: https://github.com/CellMigStandOrg/biotracks/releases
