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CellMigStandOrg / biotracks

A repository for data package representation for cell tracking data
https://pypi.python.org/pypi/biotracks
BSD 2-Clause "Simplified" License
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cell data migration open sharing tracking

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

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

.. image:: https://badge.fury.io/py/biotracks.svg :target: https://badge.fury.io/py/biotracks

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 <http://specs.frictionlessdata.io/tabular-data-package/>_ .

Installation from sources (Python 3 only)

.. code-block::

python setup.py install

Installation from PiPy

.. code-block::

pip install biotracks

Usage

Move to the scripts directory and run:

.. code-block:: bash

python create_dpkg.py your_tracking_file

This will create a tabular data package directory containing:

The latter will look like this:

.. code-block:: json

{ "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 <https://en.wikipedia.org/wiki/INI_file>_ format with two sections:

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:

.. code-block::

[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>_ .

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