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Software and System Setup

When you set up Cells2Stats on a system, you must install a static binary executable or use a Docker container. In addition to setting up Docker or a static binary compute environment that meets system requirements, you must configure the compute environment to transfer files.

System Requirements​

Operating System​

Cells2Stats is compatible with various operating systems (OS). Review the following compatibility matrix to determine the appropriate Cells2Stats distribution for your OS.

Operating SystemDocker CompatibilityStatic Binary CompatibilityOS Notes
Linux OSYes, Green CheckmarkYes, Green CheckmarkThe static binary executable is compatible with any Linux OS on an x86 architecture that uses glibc v2.19 or later.

To verify the glibc version for static binary, run the following command: ldd --version
Windows OSYes, Green CheckmarkNo, Red XWindows OS is not directly compatible with the static binary executable. Install Docker and run using Docker. Make sure to review the system requirements. Element recommends enabling the WSL 2 backend feature.
Windows OS with Windows Subsystem for Linux (WSL)Yes, Green CheckmarkYes, Green CheckmarkIf you install WSL on Windows OS, you can use the static binary executable in the WSL environment.
Mac OSYes, Green CheckmarkNo, Red XMacOS is not compatible with the static binary executable. Install Docker and run using Docker.
Note:

Cells2Stats is not supported on ARM processors.

Memory and Performance​

Software performance depends on the resources dedicated to the processing environment and if CellProfiler is enabled. For optimal performance, make sure you have at least 16 CPU cores available and enable threading Cells2Stats with the -j argument. The following memory requirements apply to both Docker and static binary distributions:

  • If CellProfiler is enabled, Cells2Stats requires 2 GB RAM per concurrent thread.
  • If CellProfiler is not enabled, Cells2Stats requires 200 MB RAM per concurrent thread.

The following benchmarks estimate the time Cells2Stats takes to regenerate output files from an AVITI24 System:

SetupTime Estimate
A non-volatile memory express (NVMe) solid-state drive (SSD) using 8 threads2 hours
An NVMe SSD using 20 threads1 hour
An Amazon c5ad.8xlarge EC2 instance with 48 virtual CPUs and onboard SSD storage< 50 minutes

The following benchmarks estimate the time Cells2Stats takes to generate CytoCanvas visualization data from an AVITI24 System:

SetupTime Estimate
A non-volatile memory express (NVMe) solid-state drive (SSD) using 8 threads<30 minutes
An NVMe SSD using 20 threads30 minutes
An Amazon c5ad.8xlarge EC2 instance with 48 virtual CPUs and onboard SSD storage< 30 minutes

Temporary Directory​

When using cloud storage, Cells2Stats downloads input files and stages output files in a temporary directory. Intermediate files generated during analysis are also stored in the temporary directory. After an execution completes, the temporary directory is cleared. The temporary directory typically uses approximately 50 GB for a typical cytoprofiling run.

By default, Cells2Stats uses the temporary directory of the OS. To change the location of the temporary directory, set the environment variable TMPDIR. Use the following example command and replace /path/to/scratch with the desired directory:

Set TMPDIR in Linux env
export TMPDIR="/path/to/scratch"

File Transfer and Storage Setup​

To transfer files, Cells2Stats requires paths to input and output locations. You can store input and output files in a local location or the cloud. For cloud storage, the following providers are compatible:

  • Amazon Web Services Simple Storage Service (AWS S3)
  • Google Cloud Storage (GCS)
  • Any rclone-compatible provider

AWS S3 and GCS storage connections require credential configuration for Cells2Stats execution. See Execute with AWS S3 and Execute with GCS for more information.

Rclone Requirements​

Rclone is a command-line program to manage files on cloud storage. Rclone provides the ability to mount any local, cloud, or virtual file system. Rclone allows Cells2Stats to access many cloud storage providers. However, Element has not tested every available rclone provider.

Follow the instructions at rclone.org/install to download and install rclone. Configure an rclone remote to communicate with your cloud storage. For more information, see the provider-specific instructions at rclone.org/#providers.

Cells2Stats Installation​

Set up Cells2Stats using Docker or static binary.

NOTE

The static binary executable for Cells2Stats is only compatible with specific OS configurations. Review the OS requirements before attempting installation.

  1. Follow the OS-specific instructions at docs.docker.com/get-docker/.

  2. Run the following command to pull the latest version of the Cells2Stats image from the Element public registry at DockerHub:

docker pull elembio/cells2stats
  1. To confirm that Cells2Stats is operational, run the following commands to display the software version and help content:
docker run elembio/cells2stats cells2stats --version
docker run elembio/cells2stats cells2stats --help
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