Cellocity is a python package that allows the user to perform Optical Flow and PIV analysis on microscopy data. It is intended to be helpful in both the exploratory and in the data acquisition phases of a cell layer dynamics project. In the exploratory phase, several different algorithms, settings, and preprocessing functions can be evaluated. In the acquisition phase, a pipeline can be "hard coded" for processing of multiple data sets through a pre-determined series of steps.
Cellocity can create vector field visualizations, speed graphs, and multiple advanced vector field analyses, such as calculating the instantaneous order parameter, alignment index and correlation lengths of migrating cells.
Documentation is available at Read the Docs. There you can also find an extensive chapter on the validation of the Cellocity software.
If you want to cite Cellocity in your work you can use our JOSS publication
