6. The cellXplorer interface

The cellXplorer is the main cellXpress window, providing access to various configuration settings and analysis tools. In addition to the main menu bar at the top, the cellXplorer window contains three task panels: Plate, Markerset and Well List.

images/Ch6_cellXplorer.png

6.1. Options: Set root path

Root paths specify the locations for the cellXpress Projects, Data and Raw Data storage directories. Using root directories for central storage makes it simple to:

  • Synchronize raw data, intermediate data or analysis results and project settings.
  • Maintain reproducible and traceable analysis workflows, all the way from the upstream raw data to the downstream results.
  • Collaborate with other users working on different operating systems (Windows or Linux); access or analyze intermediate data generated by other users.

The root directories can be set as follows:

  • [cellXplorer]: Option>Root path
images/Ch3_project-root-dir.png

6.2. Options: Parallel processing

For more efficient parallel data processing, the cellXpress supports computing with multiple processors. By default, the cellXpress will utilize all the available processors on a multiple-core machine. Alternatively, you can specify the number of processors used by the cellXpress:

  • [cellXplorer]: Options>Parallel processing
  • [cellXplorer]: Enter the number of threads or processors to use
images/Ch6_set-processor-number.png

6.3. Stop all running jobs

You can cancel a currently running job, such as cell segmentation or feature extraction, as follows:

  • [cellXplorer]: Profiling>Stop all running jobs
images/Ch6_stop-running-jobs.png