User-friendly high-content imaging analysis on a single desktop: R package H5CellProfiler

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Technological development has led to ever-increasing amounts of data in high-content screening. For utilizing such data in an efficient, thorough, and user-friendly manner we developed the R package H5CellProfiler. H5CellProfiler is based on R packages data.table, ggvis, ggplot2 and shiny. H5CellProfiler launches a browser that allows scientists to analyze large single-cell datasets and make statistical summaries and graphs on their local desktop in a fast and memory-efficient manner. In addition, single-cell track labels are calculated and broken tracks are re-connected based on user-defined thresholds resulting in unique sets of annotated tracks.

Authors 5

1. Steven Wink Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands

2. Gerhard A. Burger Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands

3. Sylvia E. Le Dévédec Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands

4. Joost B. Beltman Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands

5. Bob van de Water corresponding Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands