Move image files to be processed to a directory accessible on Rivanna (ideally /scratch).The details of CellProfiler’s batch processing strategy are explained here. If you have a large number of images that all need to be processed in the same manner, you can use Rivanna’s compute nodes for efficient non-interactive batch image processing. Non-interactive Slurm jobs for batch image processing Singularity run /scratch/$USER/cellprofiler-3.1.8.sif To start an interactive job and launch the CellProfiler graphical user interface from within the container, obtain desktop through the Open OnDemand Desktop app, start a terminal window, then run the following commands module load singularity Option B: Starting an interactive CellProfiler job Please note that this option may be very slow. Ssh -Y Continue with instructions under Starting an interactive CellProfiler job. In a terminal window on your local workstation execute the following command:.Image Pipeline Configuration Option A: ssh terminal In a Rivanna terminal window execute these commands: module load singularityĬp $CONTAINERDIR/cellprofiler-3.1.8.sif /scratch/$USER This has to be done only once and the following steps describe this process. For best performance it is recommended that users copy this container to their individual /scratch storage location. The CellProfiler container image file is provided in a shared user space. The interactive GUI mode is used to define image analysis pipelines the non-interactive mode is used for image batch processing based on previosuly configured image analysis pipelines. Please contact us for help with this package.ĬellProfiler can be run interactively with a graphical user interface (GUI) or non-interactively without any user interface. We recommend using the latest CellProfiler container version whenever possible.
Cellprofiler motion correction software#
The basic concepts of software containers, and Singularity container in particular, are explained here. Containers encapsulate applications, in this case CellProfiler, and all their required libraries isolated from the application and libraries provided by the system. The latest version of CellProfiler is available as a Singularity container. Module load singularity/3.7.1 cellprofiler/4.2.1 Module load singularity/3.7.1 cellprofiler/3.1.8 For example: module spider cellprofiler/3.1.8
Cellprofiler motion correction how to#
Module, including how to load the module, run the module spider command with the module’s full version label. The output of the command shows the available CellProfilerįor detailed information about a particular CellProfiler To find the available versions and learn how to load them, run: module spider cellprofiler CellProfiler is an image processing package to generate morphometric measurements.įor detailed information, visit the CellProfiler
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