Command-line tool

nima

Analyze a multichannel TIFF time-lapse stack.

tiffstkstr

Path to the TIFF image file.

channelslist of str, optional

Names of the channels in the TIFF image. Default is [“G”, “R”, “C”].

Saves

1. Representation of image channels and segmentation saved as BN_dim.png.

2. Plot of ratios and channel intensities for each label and background vs. time saved as BN_meas.png.

3. Table of background values saved as f_name/bg.csv.

4. Representation of background image and histogram at all time points for each channel saved as BN/bg-[C1,C2,⋯]-method.pdf.

5. For each label: Table of ratios and measured properties saved as BN/label[1,2,⋯].csv.

6. For each label: Ratio images saved as BN/label[1,2,⋯]_r[cl,pH].tif.

nima [OPTIONS] TIFFSTK [CHANNELS]...

Options

--version

Show the version and exit.

-v, --verbose

Verbosity of messages.

-s, --silent

Suppress output; verbose=0.

-o, --output <output>

Output directory path [default: ./nima-version/].

--hotpixels

Apply median filter (rad=0.5) to remove hot pixels.

-f, --flat <flat_f>

Path to flat image for shading correction.

-d, --dark <dark_f>

Path to dark image 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 [default: 10].

--bg-adaptive-radius <bg_adaptive_radius>

Radius for adaptive methods [default: X/2].

--bg-percentile <bg_percentile>

Percentile for entropy or arcsinh methods [default: 10].

--bg-percentile-filter <bg_percentile_filter>

Percentile filter for arcsinh method [default: 80].

--fg-method <fg_method>

Segmentation algorithm [default: yen].

Options:

yen | li

--min-size <min_size>

Minimum size of labeled objects [default: 2000].

--clear-border

Remove labels touching image borders [default: 0].

--wiener

Apply Wiener filter before segmentation [default: 0].

--watershed

Apply watershed binary mask (labeling) [default: 0].

--randomwalk

Apply randomwalk binary mask (labeling) [default: 0].

--image-ratios, --no-image-ratios

Compute ratio images? [default: True].

--ratio-median-radii <ratio_median_radii>

Median filter ratio images with radii [default: (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)

bima

Compute bias, dark and flat.

bima [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

-o, --output <output>

Output path [default: *.tif, *.png].

bias

Compute the BIAS frame and estimate read noise.

fpathstr

Path to the bias stack (Light Off - 0 acquisition time).

Saves

1. BIAS image (.tif): Median projection.

2. Plot (.png): Includes histograms, median projection, and visualization of hot pixels.

3. Hot pixel coordinates and values (.csv): If hot pixels are detected.

bima bias [OPTIONS] FPATH

Arguments

FPATH

Required argument

dark

Compute DARK.

fpathstr

Path to the dark stack (Light Off - Long acquisition time).

Saves

1. DARK image (.tif): Median projection.

2. Plot (.png): Includes histograms, median projection, …

bima dark [OPTIONS] FPATH

Options

--bias <bias>

File path to the bias stack (Light Off - Long acquisition time).

--time <time>

Acquisition time.

Arguments

FPATH

Required argument

flat

Flat from (.tf8) file stack.

fpathstr

Path to the (.tf8) file containing the image data.

Saves

1. FLAT image (.tif): Mean projection.

2. Plot (.png): Includes histograms, mean projection, …

bima flat [OPTIONS] FPATH

Options

--bias <bias>

Path to the bias stack (Light Off - 0 acquisition time).

Arguments

FPATH

Required argument

mflat

Compute the flat field from a collection of (.tif) files.

globpath“glob expression”

Glob pattern (enclosed in quotes) for a collection of (.tif) files.

Saves

1. FLAT image (.tif): Mean projection.

2. Plot (.png): Includes histograms, mean projection, …

bima mflat [OPTIONS] GLOBPATH

Options

--bias <bias>

Path to the bias stack (Light Off - 0 acquisition time).

Arguments

GLOBPATH

Required argument

plot

Plot profiles of a 2D image.

fpathstr

Path to the 2D image file (e.g. Bias or Dark).

Saves

A plot of profiles is saved as a ‘.png’ file.

bima plot [OPTIONS] FPATH

Arguments

FPATH

Required argument