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An end-to-end software solution for the analysis of high-throughput single-cell migration data

View Article: PubMed Central - PubMed

ABSTRACT

The systematic study of single-cell migration requires the availability of software for assisting data inspection, quality control and analysis. This is especially important for high-throughput experiments, where multiple biological conditions are tested in parallel. Although the field of cell migration can count on different computational tools for cell segmentation and tracking, downstream data visualization, parameter extraction and statistical analysis are still left to the user and are currently not possible within a single tool. This article presents a completely new module for the open-source, cross-platform CellMissy software for cell migration data management. This module is the first tool to focus specifically on single-cell migration data downstream of image processing. It allows fast comparison across all tested conditions, providing automated data visualization, assisted data filtering and quality control, extraction of various commonly used cell migration parameters, and non-parametric statistical analysis. Importantly, the module enables parameters computation both at the trajectory- and at the step-level. Moreover, this single-cell analysis module is complemented by a new data import module that accommodates multiwell plate data obtained from high-throughput experiments, and is easily extensible through a plugin architecture. In conclusion, the end-to-end software solution presented here tackles a key bioinformatics challenge in the cell migration field, assisting researchers in their high-throughput data processing.

No MeSH data available.


Related in: MedlinePlus

A typical multi-sample single-cell migration experiment loaded in CellMissy.A breast cancer cell line (BT549) was left untreated (control) or treated with a concentration range of a drug (in casu nine different concentrations of the actin drug latrunculin B). Each condition on the plate is color coded (see list bottom left and colored boxes around wells in the plate view). Data produced by image processing from the replicate wells are loaded (filled color coded wells in plate view and central list). Each replicate data set (from one well) is a collection of single-cell trajectories, as shown in the text file in the inset. The table at the bottom reports the same data after loading. It is possible to load data associated with multiple image processing algorithms (Algo, see central part of view) and/or multiple imaging types (Im).
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f2: A typical multi-sample single-cell migration experiment loaded in CellMissy.A breast cancer cell line (BT549) was left untreated (control) or treated with a concentration range of a drug (in casu nine different concentrations of the actin drug latrunculin B). Each condition on the plate is color coded (see list bottom left and colored boxes around wells in the plate view). Data produced by image processing from the replicate wells are loaded (filled color coded wells in plate view and central list). Each replicate data set (from one well) is a collection of single-cell trajectories, as shown in the text file in the inset. The table at the bottom reports the same data after loading. It is possible to load data associated with multiple image processing algorithms (Algo, see central part of view) and/or multiple imaging types (Im).

Mentions: Data are typically derived from a common multiwell plate experimental setup, as shown in Fig. 2, in which multiple conditions are tested in parallel, e.g., with different cell lines and/or different treatments, such as sets of chemical compounds, concentration ranges of a specific compound, selected libraries of siRNA and so on. Multiple technical replicates (i.e., multiple wells) are usually performed for each condition, and the module allows data visualization and analysis at both the condition and replicate level. Obviously, less complicated experiments can also be imported and analyzed. As shown in Figs 1 and 2, the module expects text files reporting four distinct columns: (i) the trajectory unique ID, (ii) the time point, (iii) the x coordinate (either in pixel or μm), and (iv) the y coordinate (either in pixel or μm). This is described in detail in a dedicated user manual at the project homepage.


An end-to-end software solution for the analysis of high-throughput single-cell migration data
A typical multi-sample single-cell migration experiment loaded in CellMissy.A breast cancer cell line (BT549) was left untreated (control) or treated with a concentration range of a drug (in casu nine different concentrations of the actin drug latrunculin B). Each condition on the plate is color coded (see list bottom left and colored boxes around wells in the plate view). Data produced by image processing from the replicate wells are loaded (filled color coded wells in plate view and central list). Each replicate data set (from one well) is a collection of single-cell trajectories, as shown in the text file in the inset. The table at the bottom reports the same data after loading. It is possible to load data associated with multiple image processing algorithms (Algo, see central part of view) and/or multiple imaging types (Im).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5304333&req=5

f2: A typical multi-sample single-cell migration experiment loaded in CellMissy.A breast cancer cell line (BT549) was left untreated (control) or treated with a concentration range of a drug (in casu nine different concentrations of the actin drug latrunculin B). Each condition on the plate is color coded (see list bottom left and colored boxes around wells in the plate view). Data produced by image processing from the replicate wells are loaded (filled color coded wells in plate view and central list). Each replicate data set (from one well) is a collection of single-cell trajectories, as shown in the text file in the inset. The table at the bottom reports the same data after loading. It is possible to load data associated with multiple image processing algorithms (Algo, see central part of view) and/or multiple imaging types (Im).
Mentions: Data are typically derived from a common multiwell plate experimental setup, as shown in Fig. 2, in which multiple conditions are tested in parallel, e.g., with different cell lines and/or different treatments, such as sets of chemical compounds, concentration ranges of a specific compound, selected libraries of siRNA and so on. Multiple technical replicates (i.e., multiple wells) are usually performed for each condition, and the module allows data visualization and analysis at both the condition and replicate level. Obviously, less complicated experiments can also be imported and analyzed. As shown in Figs 1 and 2, the module expects text files reporting four distinct columns: (i) the trajectory unique ID, (ii) the time point, (iii) the x coordinate (either in pixel or μm), and (iv) the y coordinate (either in pixel or μm). This is described in detail in a dedicated user manual at the project homepage.

View Article: PubMed Central - PubMed

ABSTRACT

The systematic study of single-cell migration requires the availability of software for assisting data inspection, quality control and analysis. This is especially important for high-throughput experiments, where multiple biological conditions are tested in parallel. Although the field of cell migration can count on different computational tools for cell segmentation and tracking, downstream data visualization, parameter extraction and statistical analysis are still left to the user and are currently not possible within a single tool. This article presents a completely new module for the open-source, cross-platform CellMissy software for cell migration data management. This module is the first tool to focus specifically on single-cell migration data downstream of image processing. It allows fast comparison across all tested conditions, providing automated data visualization, assisted data filtering and quality control, extraction of various commonly used cell migration parameters, and non-parametric statistical analysis. Importantly, the module enables parameters computation both at the trajectory- and at the step-level. Moreover, this single-cell analysis module is complemented by a new data import module that accommodates multiwell plate data obtained from high-throughput experiments, and is easily extensible through a plugin architecture. In conclusion, the end-to-end software solution presented here tackles a key bioinformatics challenge in the cell migration field, assisting researchers in their high-throughput data processing.

No MeSH data available.


Related in: MedlinePlus