Automatic SHG and PL Image Detection

Currently we support analysis of TIFF files for both Second Harmonic Generation (SHG) and Photoluminescence (PL) imaging techniques. PyFibre is able to recognise and load in the format of these images if they contain an appropriate file labelling scheme.

Images containing (non case sensitive) keywords in their file name (see below) will allow PyFibre automatically match these up based on the {prefix}:

{directory}/{prefix}-{keyword}{suffix}.tif

The files will then appear as:

{directory}/{prefix}

It is expected that files containing the keyword SHG will represent 1 greyscale image (the second harmonic signal), possibly recorded as a stack.

Files containing the keyword PL should represent 2 greyscale images (the phospholuminescene signal and its transmission record), possibly both recorded as separate stacks.

Files containing the combined SHG-PL keyword will represent 3 greyscale images (SHG, PL and transmission record), with each possibly recorded as separate stacks.

The file reader requires certain metadata to be present in the TIFF files in order to interpret which channel corresponds to each signal. Currently only TIFF files created by Olympus FluoView and ImageJ programs are supported.