Siff-to-Tiff functions

You might be using a ScanImage-FLIM microscope, but only want to use regular intensity imaging tools and analyses. SiffPy supports most of what you likely want to do, or returns a numpy array that you can just pipe in to some other pathway or analysis code, but some tools just want a plain .tiff. SiffPy provides a few simple functions to convert to .tiff. For now, it only implements the ScanImage .tiff specification (which is not OME compliant!!), but soon I will add OME-TIFF support as a keyword argument.

I will also (soon) implement a command line tool to call the siff_to_tiff Rust code directly. Not yet though!

SiffPy hosts a wrapper function for the siffreadermodule function (described below) which can be called easily

from siffpy import siff_to_tiff

my_input_path = "somewhere_like_here"
my_target_path = "this_place_looks_good/a_cool_directory"

siff_to_tiff(my_target_path, target_file = my_target_path)
siffpy.siff_to_tiff(source_file: StrLike, target_file: 'StrLike' | None = None, mode: str = 'ScanImage') → None

Converts a .siff file to a .tiff file containing only intensity information. For siffcompressed data, this should be smaller (because it just discards arrival times). For siff data that’s not too big, this will likely create a larger file.

## Arguments

  • source_filestr or str-like

    Path to a .siff file. Will immediately be converted to str

  • target_fileOptional[str-like]

    Path to where the .tiff should be saved. If None, saves to the same directory as the source file, with the same name but with the extension changed to .tiff. Otherwise immediately converted to str

  • modestr

    Can be ScanImage or (in progress) ome. ScanImage is the default. This is not OME-compliant, so ImageJ/Fiji (for example) will just parse it as a flattened image series. When ome is implemented, that mode will be readable by most bio image viewers.

Warning: the function below is autodocumented using the DOCSTRING attached to the siffreadermodule’s siff_to_tiff function, which may be out of date from the current implementation. The more reliable documentation is in the siff_to_tiff function’s stub file in siffreadermodule/__init__.pyi.

corrosiffpy.siff_to_tiff(sourcepath, savepath=None, mode='ScanImage')

Converts a .siff file to a .tiff file using the corrosiff library.