cell_track.tools.track_image module

cell_track.tools.track_image.track_lif(lif_path: str, out_path: str, model: keras.engine.training.Model) → None

Applies ML model (model object) to everything in the lif file.

This will write a trackmate xml file via the method tm_xml.write_xml(), and save output tiff image stacks from the lif file.

Parameters:

• lif_path (str) – Path to the lif file
• out_path (str) – Path to output directory
• model (str) – A trained keras.models.Model object

Returns: None

cell_track.tools.track_image.track_tiff_folder(tiff_folder: str, model: keras.engine.training.Model) → None

Applies ML model (model object) to every tiff file in the directory.

This will write a trackmate xml file via the method tm_xml.write_xml(), and save output tiff image stacks from the lif file.

Parameters:

• lif_path (str) – Path to the lif file
• out_path (str) – Path to output directory
• model (keras.models.Model) – A trained keras.models.Model object

Returns: None