title: Traxtile: Interactive editing of cell tracks in time-lapse images.
abstract: Time-lapse imaging can be used to quantify how cells move, divide, and die over time and under defined culture conditions. Open source software packages such as CellProfiler, Icy, and Fiji provide robust and convenient interfaces for performing such analyses. However, object tracking algorithms are imperfect, and validation of significant events is often required. This is challenging, as CellProfiler produces only tabular data for object tracking, and the graphical tools in Icy and Fiji are not optimal for manual review of these events. Here we describe Traxtile, a program that allows interactive graphical review and revision of object tracking assignments. Traxtile imports initial assignments and automatically identifies events needing review (i.e., apparent creation of new objects, splits, merges, and losses). For each such event, the object track is displayed on a montage of images centered on the event and spanning the preceding and subsequent frames. Links between cells in successive frames can be reviewed and edited, yielding validated tracks for the image series. Reports summarize events from the validated tracks. Traxtile is implemented in Python version 2.7 using standard distribution libraries (available at www.python.org) and is freely available at https://github.com/braunb/traxtile-public.
authors.affiliation: Department of Pediatrics, University of California, San Francisco, UCSF Benioff Children's Hospital and The Helen Diller Family Comprehensive Cancer Center, San Francisco, CA.
authors.forename: Benjamin S
authors.initials: BS
authors.lastname: Braun
mesh_terms: D000465:Algorithms; D000818:Animals; D058948:Cell Tracking / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012984:Software; D059008:Time-Lapse Imaging
keywords: CellProfiler; Fiji; Icy; Python; cell imaging; image analysis; object tracking; time lapse