Package: 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 theFrictionless Tabular Data Package.Installation from sources (Python 3 only)python setup.py installInstallation from PiPypip install biotracksUsageMove to thescriptsdirectory and run:pythoncreate_dpkg.pyyour_tracking_fileThis will create a tabular data package directory containing:a csv file for theobjects(e.g., cells)a csv file for thelinks(linear collections of objects)the json descriptor file for the data packageThe 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"}}]}}]}ConfigurationSome formats require a configuration file that specifies how to map object IDs, coordinate names, etc. This file must be in theINIformat with two sections:TOP_LEVEL_INFO: specifies a name for the data package and additional (optional) informationTRACKING_DATA: specifies how to map information from the source format to the biotracks column headersYou can provide a configuration file by passing it via the-coption tocreate_dpkg.py; if this option is not set, the script will look for abiotracks.inifile 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
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`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>`_ .