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BMC Bioinformatics. 2015 Nov 4;16:368. doi: 10.1186/s12859-015-0759-x.

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.

Author information

1
Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA. mbray@broadinstitute.org.
2
Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA. anne@broadinstitute.org.

Abstract

BACKGROUND:

Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows convenient assessment of track quality, especially for researchers tuning tracking parameters for high-content time-lapse experiments. This makes quality assessment and algorithm adjustment a substantial challenge, particularly when dealing with hundreds of time-lapse movies collected in a high-throughput manner.

RESULTS:

We present CellProfiler Tracer, a free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package. Tracer allows multi-parametric morphological data to be visualized on object tracks, providing visualizations that have already been validated within the scientific community for time-lapse experiments, and combining them with simple graph-based measures for highlighting possible tracking artifacts.

CONCLUSIONS:

CellProfiler Tracer is a useful, free tool for inspection and quality control of object tracking data, available from http://www.cellprofiler.org/tracer/.

PMID:
26537300
PMCID:
PMC4634901
DOI:
10.1186/s12859-015-0759-x
[Indexed for MEDLINE]
Free PMC Article

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