Command-line tool#
nima#
Analyze multichannel (default:[“G”, “R”, “C”]) tiff time-lapse stack.
TIFFSTK : Image file.
CHANNELS : Channel names.
Save:
(1) representation of image channels and segmentation BN_dim.png,
(2) plot of ratios and channel intensities for each label and bg vs.
time BN_meas.png,
(3) table of bg values */bg.csv,
(4) representation of bg image and histogram at all time points for
each channel BN/bg-[C1,C2,⋯]-method.pdf, and for each label:
(5) table of ratios and measured properties BN/label[1,2,⋯].csv
and (6) ratio images BN/label[1,2,⋯]_r[cl,pH].tif.
nima [OPTIONS] TIFFSTK [CHANNELS]...
Options
- --version#
Show the version and exit.
- --silent#
Do not print; verbose=0.
- -o, --output <output>#
Output path [default: ./nima/].
- --hotpixels#
Median filter (rad=0.5) to remove hotpixels.
- -f, --flat <flat_f>#
Dark for shading correction.
- -d, --dark <dark_f>#
Flat for shading correction.
- --bg-method <bg_method>#
Background estimation algorithm [default:li_adaptive].
- Options:
li_adaptive | entropy | arcsinh | adaptive | li_li
- --bg-downscale <bg_downscale>#
Binning Y X.
- --bg-radius <bg_radius>#
Radius for entropy or arcsinh methods [def:10].
- --bg-adaptive-radius <bg_adaptive_radius>#
Radius for adaptive methods [def:X/2].
- --bg-percentile <bg_percentile>#
Percentile for entropy or arcsinh methods [def:10].
- --bg-percentile-filter <bg_percentile_filter>#
Percentile filter for arcsinh method [def:80].
- --fg-method <fg_method>#
Segmentation algorithm [default:yen].
- Options:
yen | li
- --min-size <min_size>#
Minimum size labeled objects [def:2000].
- --clear-border#
Remove labels touching image borders.
- --wiener#
Wiener filter before segmentation.
- --watershed#
Watershed binary mask (to label cells).
- --randomwalk#
Randomwalk binary mask (to label cells).
- --image-ratios, --no-image-ratios#
Compute ratio images? [default:True]
- --ratio-median-radii <ratio_median_radii>#
Median filter ratio images with radii [def:(7,3)].
- --channels-cl <channels_cl>#
Channels for Cl ratio [default:C/R].
- --channels-ph <channels_ph>#
Channels for pH ratio [default:G/C].
Arguments
- TIFFSTK#
Required argument
- CHANNELS#
Optional argument(s)
bias#
Compute bias, dark and flat.
bias [OPTIONS] COMMAND [ARGS]...
Options
- --version#
Show the version and exit.
bias#
Compute BIAS frame and estimate read noise.
FPATH: the bias stack (Light Off - 0 acquisition time).
Output:
.tif BIAS image = median projection
.png plot (histograms, median, projection, hot pixels)
[.csv coordinates and values of hot pixels] if detected
bias bias [OPTIONS] FPATH
Arguments
- FPATH#
Required argument
dark#
Compute DARK.
FPATH: the bias stack (Light Off - Long acquisition time).
bias dark [OPTIONS] FPATH
Options
- --bias <bias>#
- --time <time>#
Arguments
- FPATH#
Required argument
flat#
Flat from (.tf8) file.
bias flat [OPTIONS] FPATH
Options
- --bias <bias>#
Arguments
- FPATH#
Required argument
mflat#
Flat from a collection of (.tif) files.
bias mflat [OPTIONS] GLOBPATH
Options
- --bias <bias>#
Arguments
- GLOBPATH#
Required argument
plot#
Plot profiles of 2D (Bias-Flat) image.
bias plot [OPTIONS] FPATH
Arguments
- FPATH#
Required argument