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.

added a set up vignette for converting single 3 channel images (either jpegs, tiffs, png or nd2 files) into 3 separate images (jpeg, tiff or png) per each. i.e. turning one image into three.

tutorial does an annotated single image (including measure distance), and then (silently) counts foci of large data set with significance tests

update get_pachytene to exclude late phases via eccentricity/ total area of SCs. Update count_foci to output percent of foci which colocalise with SCs

foci counting now only requires user to input the path where images are stored. Outputs a data frame with properties for each cell to do e.g. significance testing in using_synapsis_test.Rmd

attempt to fix issue #1: modify plotting orders measure_distances.R to stop plot.new not called error