registerImagesFIJI#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/image_registration.R#L683

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#

Argument

Description

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 ` options(giotto.fiji=”/some/path”)` )

DryRun

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