Tour of cellXpress

cellXplorer :: Plate navigator
cellXpress main

cellXpress cellXpress is a cellular phenotype profiling software platform developed by the Loo Lab at the Bioinformatics Institute, A*STAR, Singapore. The platform is designed for fast and high-throughput analysis of cellular phenotypes based on microscopy images.

The main graphical user interface called cellXplorer is used for project management, markerset configuration, profiling job submission, plate analysis and browsing, and well management.

cellXpress Users can choose to select different combinations of feature types, fluorescent markers, and sub-cellular regions. Fluorescence intensity values within each cell can also be converted into probability density values before feature extraction. This is especially useful for studying protein sub-cellular localization.

cellXpress options
cellXpress options

cellXpress cellXpress is designed for high-throughput imaging experiments performed in multi-well microtiter plates. It can be used to count cells, measure fluorescence intensity over the whole plates, and visualize well-to-well trend and variability.

cellViewer :: Interactive image and result viewer

cellXpress The second main graphical user interface is called cellViewer and used for visualization of multi-channel fluorescence images, segmentation, object detection and feature extraction results. It can also be used to perform interactive configuration of segmentation parameters.

cellViewer also has a split-screen display mode, which can be used to view and compare images and results from different wells side-by-side in the same windows. Users can conveniently navigate to the next frame or well through shortcut keys within cellViewer.

cellXpress viewer
cXlibrary :: customized analysis and visualization
cellXpress hdf

cellXpress Extracted features are stored in standard HDF5 format in 64-bit double precision. They can be exported as CSV files for further processing by third-party spreadsheet or data analysis software packages.

cellXpress For advanced and customized analysis, visualization and graphing, cellXpress also includes a R-interface library called cXlibrary, which can be used to import extracted features into the R environment.

The library also provides a full implementation of the SVM-based d-profiling method (Loo, et. al., Nat Methods, 2007). An example of d-profiles for siRNA knockdowns of four different categories of genes in HeLa cells is shown here (circles = genes).

cellXpress R console