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About

Introduction

This document contains the working draft of the Tracks specification being developed by the Cell Migration Standardisation Organisation (CMSO).

The current specification is based on tracking by detection techniques (see computational workflow in the following figure) and the data produced therein:

workflow{:class="img-responsive"}

  1. A segmentation algorithm detects objects of interest (i.e. cells) in a set of microscopy images (usually time-lapse), producing objects
  2. A linking algorithm finds associations between these objects and links them in time, producing links
  3. A segment linking processes the links, identifying possible events (gap-closing, split, merge), producing final tracks

This specification aims at representing these data in a tabular format:

Data is held in a table. The properties of a table are:

  • columns — the list of columns in the table
  • rows — the list of rows in the table

For a formal specification of Tabular Data Models see Model for Tabular Data and Metadata on the Web-W3C.

Goals

The goal of this specification is to define a common, standard format to represent cell tracking data associated with cell migration experiments. The specification should:

  • be simple and extensible
  • re-use existing standard formats, where possible
  • be associated with human- and machine-readable metadata

Language

The key words MUST, MUST NOT, REQUIRED, SHALL, SHALL NOT, SHOULD, SHOULD NOT, RECOMMENDED, MAY, and OPTIONAL in this specification are to be interpreted as described in RCF 2119.

Links

See the version 0.1 of this specification.