Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Nov 4:16:368.
doi: 10.1186/s12859-015-0759-x.

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

Mark-Anthony Bray  1 , Anne E Carpenter  2
Affiliations

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

Mark-Anthony Bray et al. BMC Bioinformatics. .

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/.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
The CellProfiler Tracer interface. The user interface is divided into the (a) XYT panel, showing the object trajectories in (x,y,t) coordinates, color-coded here by the frame number; the trajectories can be color-coded to be any cell measurement of interest; (b) the lineage tree panel, highlighting the ancestor/progeny relationships corresponding to the trajectories in (a), and (c) the control panel containing various display tools. Other visualizations include (d) synchrograms of selected cells, as well as heatmaps (shown in Fig. 2)
Fig. 2
Fig. 2
Heatmap of high-content cellular time-lapse measurements. The per-nucleus measurements from a Drosophila time-lapse movie are averaged over all nuclei for each timepoint; the measurements were collected by CellProfiler software. Feature values were normalized from 0 to 1 for visualization purposes. Feature names were omitted for conciseness but are provided in the Tracer display; the features shown are listed in order in the Additional file 3: Table S1, and are further described in the CellProfiler documentation
Fig. 3
Fig. 3
Schematics of tracking errors. a An inset of the lineage panel for a movie of MCF-7 cells, with various tracking topologies highlighted. b-d Tracking errors are reflected in synchrograms of MCF-7 nuclei (top panel) and graph topologies (bottom panel) with color indicating the unique object label. b Typical graphs with no tracking errors. c Mis-segmentation of neighboring objects produces transient merging and erroneous object creation. d A brief mis-segmentation of an object results in a transient (and incorrect) split
See this image and copyright information in PMC

References

    1. Spiller DG, Wood CD, Rand DA, White MRH. Measurement of single-cell dynamics. Nature. 2010;465:736–745. doi: 10.1038/nature09232. - DOI - PubMed
    1. Neumann B, Walter T, Hériché J-K, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wünsche A, Satagopam V, Schmitz MHA, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters J-M, Hyman AA, Durbin R, Pepperkok R, Ellenberg J. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature. 2010;464:721–727. doi: 10.1038/nature08869. - DOI - PMC - PubMed
    1. Meijering E, Dzyubachyk O, Smal I. Methods for cell and particle tracking. Methods Enzymol. 2012;504:183–200. doi: 10.1016/B978-0-12-391857-4.00009-4. - DOI - PubMed
    1. Winter M, Wait E, Roysam B, Goderie SK, Ali RAN, Kokovay E, Temple S, Cohen AR. Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. Nat. Protoc. 2011;6:1942–1952. doi: 10.1038/nprot.2011.422. - DOI - PMC - PubMed
    1. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM. Cell Profiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7:R100. doi: 10.1186/gb-2006-7-10-r100. - DOI - PMC - PubMed

Publication types

LinkOut - more resources