auto_crop_fast now has a new input called cropping_factor. It defaults to 1 (which is how the size of the cropped square around the blob was previously determined, using 1* characteristic blob radius). Likely need to set e.g. cropping_factor = 1.3, once blob_factor has been chosen etc

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

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