measure distances function outputs data frame with pass and fails. count foci includes an estimate of foci NOT colocalizing in cell area

when knitting count_foci with annotate = on, includes a 2 channel image which only contains coincident foci

add optional input test_amount in auto_crop, where it only crops this number of original images. designed for troubleshooting parameter choices etc

add optional input test_amount in auto_crop, where it only crops this number of original images. designed for troubleshooting parameter choices etc

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

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

all functions documented and can be built (with documentation) successfully in Rstudio using -install and restart- and then devtools::document()

all functions documented and can be built (with documentation) successfully in Rstudio using -install and restart- and then devtools::document()

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