Index

Symbols

--bg-adaptive-radius nima command line option --bg-downscale nima command line option --bg-method nima command line option --bg-percentile nima command line option --bg-percentile-filter nima command line option --bg-radius nima command line option --bias bima-dark command line option bima-flat command line option bima-mflat command line option --channels-cl nima command line option --channels-ph nima command line option --clear-border nima command line option --dark nima command line option --fg-method nima command line option --flat nima command line option --hotpixels nima command line option --image-ratios nima command line option --min-size nima command line option

--no-image-ratios nima command line option --output bima command line option nima command line option --randomwalk nima command line option --ratio-median-radii nima command line option --silent nima command line option --time bima-dark command line option --verbose nima command line option --version bima command line option nima command line option --watershed nima command line option --wiener nima command line option -d nima command line option -f nima command line option -o bima command line option nima command line option -s nima command line option -v nima command line option

A

adaptive_radius (nima.segmentation.BgParams attribute)

arcsinh_perc (nima.segmentation.BgParams attribute) ave() (in module nima.utils)

B

bg (nima.segmentation.BgResult attribute) bg() (in module nima.nima) (in module nima.utils) BgParams (class in nima.segmentation) BgResult (class in nima.segmentation) bima command line option --output --version -o bima-bias command line option FPATH

bima-dark command line option --bias --time FPATH bima-flat command line option --bias FPATH bima-mflat command line option --bias GLOBPATH bima-plot command line option FPATH

C

calculate_bg() (in module nima.segmentation) calculate_bg_iteratively() (in module nima.segmentation) channel_mean() (in module nima.utils)

CHANNELS nima command line option clip (nima.segmentation.BgParams attribute) correct_hotpixel() (in module nima.nima)

E

erosion_disk (nima.segmentation.BgParams attribute)

F

figures (nima.segmentation.BgResult attribute) fit_gaussian() (in module nima.segmentation) FPATH bima-bias command line option bima-dark command line option bima-flat command line option bima-plot command line option

G

gen_bias() (in module nima.generat) gen_flat() (in module nima.generat) gen_frame() (in module nima.generat) gen_object() (in module nima.generat)

gen_objs() (in module nima.generat) geometric_mean_filter() (in module nima.segmentation) GLOBPATH bima-mflat command line option

H

hotpixels() (in module nima.nima)

I

ImageObjsParams (class in nima.generat)

iqr (nima.segmentation.BgResult attribute)

K

kind (nima.segmentation.BgParams attribute)

M

mask_all_channels() (in module nima.utils) measure() (in module nima.nima) median() (in module nima.nima) module nima nima.generat nima.io nima.nima nima.nima_types nima.segmentation nima.utils

N

nima module nima command line option --bg-adaptive-radius --bg-downscale --bg-method --bg-percentile --bg-percentile-filter --bg-radius --channels-cl --channels-ph --clear-border --dark --fg-method --flat --hotpixels --image-ratios --min-size --no-image-ratios --output --randomwalk --ratio-median-radii --silent --verbose --version --watershed --wiener -d -f -o -s -v CHANNELS TIFFSTK

nima.generat module nima.io module nima.nima module nima.nima_types module nima.segmentation module nima.utils module

P

perc (nima.segmentation.BgParams attribute) plot_img() (in module nima.nima) plot_meas() (in module nima.nima)

plt_img_profile() (in module nima.nima) plt_img_profile_2() (in module nima.nima) prob() (in module nima.segmentation) process_watershed() (in module nima.nima)

R

radius (nima.segmentation.BgParams attribute) ratio() (in module nima.nima)

ratio_df() (in module nima.utils) read_image() (in module nima.io) run_simulation() (in module nima.generat)

S

safe_call() (in module nima.generat) sd (nima.segmentation.BgResult attribute)

segment() (in module nima.nima) shading() (in module nima.nima)

T

TIFFSTK nima command line option