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count_foci has individual mask routines. More modular and closer to bioconductor standards. Mask routines can be called with different settings for exceptional cases e.g. after removing XY, low background and low signal

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