README.md

starfish-analysis

This repo contains recipes for processing spaceTX data using starfish on a single FOV

Format Specification

A recipe should be a python .py file containing a single method

def process_fov(fov_num: int, experiment_str: str):
    """Process a single field of view of starfish data
    Parameters
    ----------
    fov_num : int
        the field of view to process
    experiment_str : int
        path of experiment json file

    Returns
    -------
    DecodedSpots :
        tabular object containing the locations of detected spots.
    """

At the top of the file the recipe should also include the url location of the full experiment data.

An example recipe.py file can be found here

Special processing

If an experiment requires processing data on a per round/ch/zplane basis within a fov the single method within the provided recipe file should include the round/ch/zplane number as an extra parameter to the process_fov method.

An example of a recipe.py that processes per round within a fov can be found here