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

Bray MA, Carpenter AE - BMC Bioinformatics (2015)

Bottom Line: Time-lapse analysis of cellular images is an important and growing need in biology.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.

View Article: PubMed Central - PubMed

Affiliation: Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA. mbray@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/.

No MeSH data available.


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
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Fig2: 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

Mentions: 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)


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

Bray MA, Carpenter AE - BMC Bioinformatics (2015)

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
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4634901&req=5

Fig2: 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
Mentions: 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)

Bottom Line: Time-lapse analysis of cellular images is an important and growing need in biology.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.

View Article: PubMed Central - PubMed

Affiliation: Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA. mbray@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/.

No MeSH data available.