auto_crop and get_pachytene gives same results for any input resolution, i.e. images found at the end of the pipeline are all the same

added option to specify an output path path_out in auto_crop_fast, get_pachytene in case user wants output crops in a different place to the original image files

add an inout parameter artificial_amp_factor in count_foci, which amplies the foci channel for annotation purposes only. Defaults to 1

measure_distances_general prints file and shows original cell image before displaying individual strands

update vignette to emphasise that count_foci and measure_distances_general find the coincident foci mask with the exact same input parameters, and it is much faster to play around with/ calibrate your input parameters with count_foci, since at the moment measure_distances_general is relatively very slow

update vignette to emphasise that count_foci and measure_distances_general find the coincident foci mask with the exact same input parameters, and it is much faster to play around with/ calibrate your input parameters with count_foci, since at the moment measure_distances_general is relatively very slow

add example usage to documentation. Single functions for auto_crop and measure_distance.  Passes BiocCheck with 0 errors, 0 warnings and 5 notes.

count_foci has crowded_foci option (TRUE/FALSE) which determines whether foci channel is smoothed (FALSE). Defaults to FALSE