do.add.masks: do.add.masks

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis.

do.add.masks

Description

do.add.masks

Usage

do.add.masks(
  dat,
  mask.dir,
  mask.pattern,
  mask.label,
  correct.extent = TRUE,
  flip.y = TRUE,
  value.modifier = 65535,
  HDF5 = FALSE,
  array = FALSE
)

Arguments

dat	NO DEFAULT. A list of spatial data objects
mask.dir	NO DEFAULT. Directory of mask files.
mask.pattern	NO DEFAULT. A character pattern that identifies the mask type (e.g. '_mask')
mask.label	NO DEFAULT. What do you want to call the mask
correct.extent	DEFAULT = TRUE
flip.y	DEFAULT = TRUE
value.modifier	DEFAULT = 65535
HDF5	DEFAULT = FALSE. Can read in HDF5 mask files if desired (advanced use).
array	DEFAULT = FALSE. If the mask TIFF is an array (advanced use).

Author(s)

Thomas M Ashhurst, [e-mail]

References

https://github.com/ImmuneDynamics/Spectre.

ImmuneDynamics/Spectre documentation built on Nov. 12, 2023, 8:12 a.m.