molyso Developer Documentation¶
See README/and documentation for end user information. See License for license information.
A short starting point to understanding molyso’s internal structure:
molyso.mm module contains the Mother Machine specific code,
as well as the main function (see highlevel.py).
Analysis code is basically split into two levels: an OOP representation of the data analyzed, as well as some
core functions (functional) which perform individual processing step.
molyso.mm.channel_detection.Channel class calls a
which returns mere numbers, of which the class constructs
molyso.generic contains a mix of library functions necessary to perform these tasks,
coarsely these can be separated into signal processing etc. functionality, and general utility functions.
molyso.debugging contains the DebugPlot class, a thin abstraction layer over matplotlib which allows for conditional, context manager based plot generation.
molyso.imageio contains the image reading functionality. The MultiImageStack is a base class and factory for opening, multi dimensional images. molyso contains reading code to open plain TIFF and OME-TIFF files, using tifffile.py. MultiImageStack acts as a implementation registry as well, if other formats should be supported, a reader subclass has to be generated, and registered at MultiImageStack. It then can automatically be used by molyso to open the format.
As mentioned earlier, the main function is within highlevel.py. It can divert program flow to two additional modes, which overtake if called: ground truth or interactive mode.
Processing itself is handled within highlevel.py.
Doctests can be called by calling the molyso.test module.
- molyso.debugging package
- molyso.generic package
- molyso.imageio package
- molyso.mm package
- molyso.mm.cell_detection module
- molyso.mm.channel_detection module
- molyso.mm.fluorescence module
- molyso.mm.highlevel module
- molyso.mm.highlevel_interactive_ground_truth module
- molyso.mm.highlevel_interactive_viewer module
- molyso.mm.image module
- molyso.mm.tracking module
- molyso.mm.tracking_infrastructure module
- molyso.mm.tracking_output module
- molyso.test package