View source: R/image_registration.R
registerImagesFIJI | R Documentation |
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
)
source_img_dir |
Folder containing images to be registered |
output_img_dir |
Folder to save registered images to |
transforms_save_dir |
(jython implementation only) Folder to save transforms to |
ref_img_name |
(jython implementation only) File name of reference image for the registration |
init_gauss_blur |
Point detector option: initial image blurring |
steps_per_scale_octave |
Point detector option |
min_img_size |
Point detector option |
max_img_size |
Point detector option |
feat_desc_size |
Feature descriptor option |
feat_desc_orient_bins |
Feature descriptor option |
closest_next_closest_ratio |
Feature descriptor option |
max_align_err |
Geometric consensus filter option |
inlier_ratio |
Geometric consensus filter option |
headless |
Whether to have ImageJ/Fiji running headless #TODO |
batch |
Use batch mode #TODO |
MinMem, MaxMem |
Memory limits |
IncrementalGC |
Whether to use incremental garbage collection |
Threads |
Number of threads |
fijiArgs |
Arguments for ImageJ/FIJI |
javaArgs |
Arguments for Java |
ijArgs |
Arguments for ImageJ |
jython |
Use jython wrapper script |
fijiPath |
Path to fiji executable (can be set by
|
DryRun |
Whether to return the command to be run rather than actually executing it. |
This function was adapted from runFijiMacro function in jimpipeline by jefferislab
list of registered giotto objects where the registered images and spatial locations
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