admbarre / phenix_tools

Tools for interfacing with Opera Phenix outputs

phenix_tools

Set of tools to more easily interact with imaging experiments carried out on Opera Phenix microscope platform.

Usage (import module into Jupyter Notebook)

• Provide the top level experiment directory
• Inspect the summarized details by printing the experiment

• Inspect the general plate layout by using get_layout()

• Provide rules for the coating as well as the cells and other media conditions
  • NOTE: this is to be moved into a separate plate coating module

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• Group files according to metadata for easier reading and pipelining into ImageJ