## ----setup-------------------------------------------------------------------- library(knitr) library(rmarkdown) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") ## ----eval = FALSE------------------------------------------------------------- # BiocManager::install("synapsis") ## ----eval = FALSE------------------------------------------------------------- # library(devtools) ## ----eval = FALSE------------------------------------------------------------- # devtools::install_git('https://github.com/mcneilllucy/synapsis', dependencies = TRUE) ## ----------------------------------------------------------------------------- library(synapsis) ## ----eval = FALSE------------------------------------------------------------- # ??auto_crop_fast ## ----------------------------------------------------------------------------- path = paste0(system.file("extdata",package = "synapsis")) ## ----------------------------------------------------------------------------- library(EBImage) ## ----------------------------------------------------------------------------- file_MLH3 <- paste0(path,"/MLH3rabbit488_SYCP3mouse594_fancm_fvb_x_fancm_bl6_724++_slide01_006-MLH3.tif") image_MLH3 <- readImage(file_MLH3) ## ----eval = FALSE------------------------------------------------------------- # display(2*image_MLH3) ## ----------------------------------------------------------------------------- file_SYCP3 <- paste0(path,"/MLH3rabbit488_SYCP3mouse594_fancm_fvb_x_fancm_bl6_724++_slide01_006-SYCP3.tif") image_SYCP3 <- readImage(file_SYCP3) ## ----eval = FALSE------------------------------------------------------------- # display(2*image_SYCP3) ## ----------------------------------------------------------------------------- cat("dimension of image:", dim(image_MLH3)[1], " x ", dim(image_MLH3)[2], sep = " ") ## ----------------------------------------------------------------------------- mb = 1e06 cat("file size in mb:", file.size(file_MLH3)/mb, sep = " ") ## ----------------------------------------------------------------------------- auto_crop_fast(path, annotation = "on", max_cell_area = 30000, min_cell_area = 7000, file_ext = "tif") ## ----------------------------------------------------------------------------- unlink(paste0(path,"/crops-RGB/"), recursive = TRUE) unlink(paste0(path,"/crops/"), recursive = TRUE) ## ----------------------------------------------------------------------------- auto_crop_fast(path, annotation = "on", max_cell_area = 30000, min_cell_area = 7000, file_ext = "tif",crowded_cells = TRUE) ## ----------------------------------------------------------------------------- SYCP3_stats <- get_pachytene(path,ecc_thresh = 0.8, area_thresh = 0.04, annotation = "on",file_ext = "tif") ## ----------------------------------------------------------------------------- foci_counts <- count_foci(path,offset_factor = 8, brush_size = 3, offset_px = 0.6, brush_sigma = 3, annotation = "on", stage = "pachytene",file_ext = "tif", watershed_stop= "on", crowded_foci = FALSE, C1 = 0.03, disc_size_foci = 9) ## ----------------------------------------------------------------------------- print(foci_counts) ## ----------------------------------------------------------------------------- unlink(paste0(path,"/crops-RGB/"), recursive = TRUE) unlink(paste0(path,"/crops/"), recursive = TRUE)