registerImagesFIJI#
Last Updated: Oct 02, 2023
Description#
Wrapper function for Register Virtual Stack Slices plugin in FIJI
Usage#
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
)
Arguments#
|
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
|
|
Whether to return the command to be run rather than actually executing it. |
Details#
This function was adapted from runFijiMacro function in jimpipeline by jefferislab
Value#
list of registered giotto objects where the registered images and spatial locations