Python utils to process imaging data collected with Opera Phenix at FIMM High Content Imaging and Analysis (FIMM-HCA) unit.
ConvertToStack.py, Deconvolution.py, FindFocalPlane.py and MIP.py are the processing modules which can be executed either from the command line (check the arguments from the source code) or used in object-oriented fashion as is done in the main pipeline script runOperaPhenix.py.
- ConvertToStack.py: Creates multi-channel 3D OME-TIFF stacks from 2D images using imgcnv.
- Deconvolution.py: Runs deconvolution of 3D stacks using DeconvolutionLab2 library.
- FindFocalPlane.py: Finds and extracts the most sharp focal plane from 3D stack.
- MIP.py: Creates maximum intensity projections of each 3D stack.
- OPUtils.py: Support class used in various processing classes.
- configuration.cfg: Includes necessary parameters for different processing steps, paths to libraries and file path patterns.
- runOperaPhenix.py: Main script to run image preprocessing pipeline. The script is executed without arguments.
The package requires Python3.5 or newer, and some basic libraries such as numpy, scipy, pandas and imageio. Deconvolution requires DeconvolutionLab2 library and converting 2D images to 3D multi-channel stack requires imgcnv.