5. Exporting cellXpress data

Image processing and analysis with the cellXpress will produce one or more of the following types of data:

The cellXpress saves this data as binary HDF5-format files in the directory of the associated project, with a ".cX*" file extension. You can view cX* data files directly using the HDFView tool, or load the data into another software package, such as R, for futher analysis.

5.1. Browsing cellXpress data using HDFView

The HDF5 file format permits compact storage of numerical data in hierarchical or structured format. Typically, each HDF5-format cX* file contains data for a single well from a plate. Each file is encoded hierarchically, with data "groups" that correspond to individual image frames from the corresponding well. These "data groups" contain the measured or computed feature or segmentation data as numerical arrays.

To view a cellXpress data file using HDFView:

  • Download the HDFView tool and follow instructions to install it.
  • Start the HDFView program and use it to open the cX* file you wish to view.

5.2. Loading cellXpress data into R

The cellXpress platform provides custom functions for importing cX* data files into R. To make use of these, the R package h5r (available for both Windows and Linux) must be installed. An example of how to load cX data into R is given in Chapter 8 (LINK).