View source: R/spots_combined.R
spots.combined.file | R Documentation |
Find spots using information from two channels
spots.combined.file( file, size = NULL, voxelsize = NULL, folder = "./", thresh.offset = 0.1, min.sum.intensity = 2, max.distance = 0.5, use.brightest = FALSE, max.spots = 2, full.voxel = FALSE, output = "markers" )
file |
File name |
size |
size of img in microns, if size and voxelsize are NULL, size is determined from folder XYZmic |
voxelsize |
size of voxel in microns |
folder |
Folder |
thresh.offset |
Thresh offset used in EBImage::thresh() |
min.sum.intensity |
spots smaller than min.sum.intensity are ignored |
max.distance |
use only spots with distance to other color spot smaller than max.distance |
use.brightest |
Logical; use only brightest in max.distance? |
max.spots |
maximum of spots (per channel), only when use brightest=TRUE |
full.voxel |
Logical; output contains full voxel instead of rgb intensities |
output |
output folder |
RGB image with spots will be written to output folder
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