CytoTable

[maxulysse]

Description of feature

cytotable should be in this pipeline

[d33bs]

CytoTable is a tool which enables feature integration from image-based analysis feature extraction tools, such as CellProfiler and DeepProfiler. It prepares data for use by image-based profilers such as Pycytominer(as seen in #9, #10, #12 , #11). It also prepares data which may be read using coSMicQC (as seen in #8). From a workflow perspective it likely would be best implemented after CellProfiler feature extraction (CSV's, SQLite, etc)(perhaps after a step focused on #6).

CytoTable includes documentation to help outline how it should be used here: https://cytomining.github.io/CytoTable/tutorial.html . Please also note there are a number of presets available depending on the data source and type which is needed. These presets may be specified and optionally overridden at runtime using the cytotable.convert(...,preset="<name>", ...) parameter.

Note: CytoTable may be used in multithreaded or multiprocess modes by way of Parsl configurations which can be passed as a parameter to CytoTable (cytotable.convert(..., parsl_config ="<name>", ...)). Depending on how tasks are implemented in Nextflow, this could be an important consideration (for ex. how many threads vs cores are available to the environment).