Welcome to SiffPy’s documentation!

This readthedocs documentation contains information on:

• how to install SiffPy

• how to use SiffPy to generate arrays of data from .siff files

• analyses on those data using the trace_analysis tools in siffmath

• How the C++ siffreadermodule extension module works

These tools are used to read and manipulate data in .siff files (ScanImage-FLIM format).

Installation:

• Installing SiffPy
  • pip
  • conda
• Additional (optional) dependencies

Tutorials:

• An introduction to SiffPy
  • File I/O
  • Registration
• Masking methods
• Analysis with Trace-type objects
• Fitting FLIM Parameters
  • Fit a single exponential
  • Fitting two exponentials
  • Add background noise
  • Pushing it to the limit
  • Multiple pulses
  • Now we can try it with the MultiPulseFLIMParams
  • Multiple fluorophores and multiple pulses
  • The final boss: multiple channels, multiple fluorophores, multiple pulses
• Siff-to-Tiff functions
  • siff_to_tiff()
  • siff_to_tiff()

Troubleshooting:

• Common issues

Main classes:

• SiffReader API
  • SiffReader
• ImParams API
  • ImParams
• FLIMParams classes
  • Initialization of the FLIMParams class
  • FlimUnits and the as_units context manager
  • Saving FLIMParams
• Traces API
  • FluorescenceTrace
  • FluorescenceVector
  • FlimTrace
• siffreadermodule API (old C++ extension module)
  • SiffIO
• RegistrationInfo classes
  • Core implementation
  • Saving and loading
  • Calling with SiffReader

Indices and tables

• Index

• Module Index

• Search Page