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Biotracks: a standard format for cell migration-derived tracking files

https://travis-ci.org/CellMigStandOrg/biotracks.svg?branch=master

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_file

This 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: