PySOFI Reference Manual

Introduction

PySOFI consists of 8 modules, each contains a group of functions relevant to the module, and a main data class(pysofiData, encapsulated in pysofi.py) that integrates the function steps from each module to perform SOFI analyses. Such design enables flexible composition of different SOFI analysis routines through the pysofiData class. Extensions of extra functionalities can be implemented as extra.py modules to the PySOFI package, and integrated by implementing the relevant methods and attributes to the pysofiData class.

In summary, PySOFI contains various function modules relevant to SOFI analysis: * reconstruction.py provides capabilities for moments and SOFI cumulants calculations. The cumulant calculation is implemented using recursive relations and is capable of calculating cumulants up to arbitrary orders. It also provides functions for bleaching correctionof a .tiff movie necessary where bleaching of the signal level greatly influences the validity of SOFI cumulants.

• finterp.py

provides Fourier interpolation on .tiff stacks for fSOFI processing.pysofi also contains the modules for SOFI 2.0 calculations listes below.

• filtering.py

for pixel-wise noise filtering along the time axis.

• deconvsk.py

provides functions forshrinking kernel deconvolution (DeconvSK, non-peer reviewed).

• ldrc.py

provides local dynamic range compression (ldrc) of images with large dynamic range of pixel values.

• visualization.py

module is implemented for interactive visualization of the results using Bokeh.

Detailed examples for each module will be discussed in our paper and on Github, each accompanied with a tutorial implemented in Jupyter notebook (see Demos)).

Modules

• PysofiData class
  • Attributes and Methods
  • Load Data
• Fourier Interpolation
  • Functions
  • Examples
• Reconstructions
  • Functions
  • Examples
• Noise Filtration
  • functions
  • Example
• Shrinking Kernel Deconvolution (DeconvSK, non-peer reviewed)
  • functions
  • Example
• LDRC Method
  • Functions
  • Example
• Multi-Order Cumulant Analysis (MOCA, non-peer reviewed)
  • Functions
  • Example
• Result visualizations
  • Functions
  • Examples
• Filtering Masks
  • Functions
  • Examples