towbintools_pipeline

towbintools_pipeline is a modular pipelining tool made to streamline the analysis of C. elegans time lapse microscopy experiments. It includes :

• robust and human readable configuration system for reproducible image analysis pipeline

• state of the art deep learning segmentation

• tools to easily retrain and fine tune said segmentation models

• a GUI for annotating time series (i.e. molts)

• convenient plotting in jupyter notebooks with ready made functions

Head to the Getting Started section to learn how to install the pipeline, how to use building blocks and how to run your first pipeline.

You can find information on how to customize the pipeline execution, retrain models or use the GUI or in the Usage section

The Building Block sections contains detailed explanation of all the parameters of every block.