Wrapper function for Register Virtual Stack Slices plugin in FIJI
registerImagesFIJI(
source_img_dir,
output_img_dir,
transforms_save_dir,
ref_img_name,
init_gauss_blur = 1.6,
steps_per_scale_octave = 3,
min_img_size = 64,
max_img_size = 1024,
feat_desc_size = 8,
feat_desc_orient_bins = 8,
closest_next_closest_ratio = 0.92,
max_align_err = 25,
inlier_ratio = 0.05,
headless = FALSE,
batch = TRUE,
MinMem = MaxMem,
MaxMem = 2500,
IncrementalGC = TRUE,
Threads = NULL,
fijiArgs = NULL,
javaArgs = NULL,
ijArgs = NULL,
jython = FALSE,
fijiPath = fiji(),
DryRun = FALSE
)
Folder containing images to be registered
Folder to save registered images to
(jython implementation only) Folder to save transforms to
(jython implementation only) File name of reference image for the registration
Point detector option: initial image blurring
Point detector option
Point detector option
Point detector option
Feature descriptor option
Feature descriptor option
Feature descriptor option
Geometric consensus filter option
Geometric consensus filter option
Whether to have ImageJ/Fiji running headless #TODO
Use batch mode #TODO
Memory limits
Whether to use incremental garbage collection
Number of threads
Arguments for ImageJ/FIJI
Arguments for Java
Arguments for ImageJ
Use jython wrapper script
Path to fiji executable (can be set by
options(giotto.fiji="/some/path")
)
Whether to return the command to be run rather than actually executing it.
list of registered giotto objects where the registered images and spatial locations
This function was adapted from runFijiMacro function in jimpipeline by jefferislab