CellSignalingTools-package: Analyze Fluoresence Microscopy Data and Scientific Images for...

In dami82/CellSignalingTools: Analysis of Images for Molecular Biology Applications

Description

Analyze Fluoresence Microscopy data and calculate nuclear to cytoplasmic signal ratios based on signal profiles or stacked immunofluorescence TIFF images.

Author(s)

Damiano Fantini <[e-mail]>

References

http://www.biotechworld.it/bioinf/2016/03/09/analyzing-fluoresence-microscopy-data-with-r/

Examples

####-------- Example 01: IF data analysis ----------------
####
data("leio_cells_dapi")
data("leio_cells_green")
dapi_mask <- get_dapi_range(leio_cells_dapi, 0.05)
d_msk <- dapi_mask[800:1100, 800:1100]
g_img <- leio_cells_green[800:1100, 800:1100]
nc_signal <- apply_mask(g_img, d_msk, bckgrnd = 0.05)
nc_ratio_tiff(nc_signal)
plot_signal(nc_signal)
####
####-------- Example 02: signal profile analysis ---------
####
data("leio_basal_profile")
data("leio_pq100_profile")
items <- list(leio_basal_profile, leio_pq100_profile)
conditions <- c('CTR','PQ100')
results <- lapply(1:2, (function(n){
  nc_ratio_profile(items[[n]], 
  "baseline",
  "mean", 
  conditions[n], 
  "PTEN", 
  0.065)
})) 

dami82/CellSignalingTools documentation built on May 14, 2019, 3:32 p.m.