Description Usage Arguments Value
View source: R/spots_combined.R
Find spots using information from two channels for folder
1 2 3 4 5 6 7 8 9 10 11 12 13 | spots.combined.folder(
path,
size = NULL,
voxelsize = NULL,
thresh.offset = 0.1,
min.sum.intensity = 2,
max.distance = 0.5,
use.brightest = FALSE,
max.spots = 2,
full.voxel = FALSE,
output = "markers",
cores = 1
)
|
path |
path to folder |
size |
size of img in microns, if size and voxelsize are NULL, size is determined from folder XYZmic |
voxelsize |
size of voxel in microns |
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 |
cores |
number of cores we can use of parallel computing (needs parallel package if cores>1) |
RGB image with spots will be written to output folder
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