Intensity correction

Intensity correction for data with inhomogeneity issues. Performs correction on CLARITY tiff data in parallel using N4.

1. Creates a downsampled nifti from the tiff data

2. Runs N4 ‘bias field’/intensity correction on the nifti file

3. Up-samples the output bias field and applies it to the tiff data

Command-line

Usage:

$ miracl utils int_corr -f [ input_tiff_folder ] -od [ output_folder ] -s [ shrink_factor] -cn [ channel_num ] -cp [ channel_prefix ] -p [ power ]

Example:

$ miracl utils int_corr -f tiff_folder -od bias_corr_folder

Required arguments:

Flags	Description	Default Default
-f, –folder	Input CLARITY TIFF folder/dir	No default. Input folder must be provided by user.

Optional arguments:

Flags	Description	Default
-od, --outdir	Output folder name	int_corr_tiffs
-cn, --channum	Chan # for extracting single channel from multiple channel	data  1
-cp, --chanprefix	Chan prefix (string before channel number in file name). Example: C00	None
-ch, --channame	Output chan name	AAV
-on, --outnii	Output nii name (script will append downsample ratio & channel info to given name)
-vx, --resx	Original resolution in x-y plane in	um  5
-vz, --resz	Original thickness (z-axis resolution/spacing between slices) in um	5
-m, --maskimg	Mask images before	correction  1
-s, --segment	Perform level-set seg using brain mask to get a dilated	one  0
-d, --down	Downsample/shrink factor to run bias corr on downsampled	data 5
-n, --noise	Noise parameter for histogram sharpening - deconvolution	0.005
-b, --bins	Histogram bins	200
-k, --fwhm	FWHM for histogram sharpening - deconvolution	0.3
-l, --levels	Number of levels for	convergence  4
-it, --iters	Number of iterations per level for convergence	50
-t, --thresh	Threshold per iteration for	convergence  0
-p, --mulpower	Use the bias field raised to a power of p to enhance its effects	1.0