DEXP Commands

add
check
copy
deconv
deskew
deskew
fuse
info
info
info
projrender
stabilize
speedtest
stabilize
tiff
view

add 

Adds the channels selected from INPUT_PATHS to the given output dataset (created if not existing).

add [OPTIONS] [INPUT_PATHS]...

Options

-c, --channels <channels>: list of channels, all channels when ommited.

-o, --output-path <output_path>: Required

-rc, --rename-channels <rename_channels>: You can rename channels: e.g. if channels are ‘channel1,anotherc’ then ‘gfp,rfp’ would rename the ‘channel1’ channel to ‘gfp’, and ‘anotherc’ to ‘rfp’

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of target

Default: False

-p, --projection, -np

If flags should be copied.

Default: True

Arguments

INPUT_PATHS: Optional argument(s)

check 

Checks the integrity of a dataset.

check [OPTIONS] [INPUT_PATHS]...

Options

-c, --channels <channels>: list of channels, all channels when ommited.

Arguments

INPUT_PATHS: Optional argument(s)

copy 

Copies a dataset, channels can be selected, cropping can be performed, compression can be changed, …

copy [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-c, --channels <channels>: list of channels, all channels when ommited.

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-wk, --workers <workers>

Number of worker threads to spawn. Negative numbers n correspond to: number_of _cores / |n|

Default: -4

-zl, --zerolevel <zerolevel>

‘zero-level’ i.e. the pixel values in the restoration (to be substracted)

Default: 0

-wkb, --workersbackend <workersbackend>

What backend to spawn workers with, can be ‘loky’ (multi-process) or ‘threading’ (multi-thread)

Default: threading

Arguments

INPUT_PATHS: Optional argument(s)

deconv 

Deconvolves all or selected channels of a dataset.

deconv [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-c, --channels <channels>: list of channels, all channels when ommited.

-d, --devices <devices>

Sets the CUDA devices id, e.g. 0,1,2 or ‘all’

Default: all

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-ts, --tilesize <tilesize>

Tile size for tiled computation

Default: 320

-m, --method <method>

Deconvolution method: for now only lr (Lucy Richardson)

Default: lr

-i, --iterations <iterations>

Number of deconvolution iterations. More iterations takes longer, will be sharper, but might also be potentially more noisy depending on method. The default number of iterations depends on the other parameters, in particular it depends on the choice of backprojection operator. For ‘wb’ as little as 3 iterations suffice.

Default: 5

-mc, --max-correction <max_correction>: Max correction in folds per iteration. By default there is no limit

-pw, --power <power>

Correction exponent, default for standard LR is 1, set to >1 for acceleration.

Default: 1.0

-bs, --blind-spot <blind_spot>

Blindspot based noise reduction. Provide size of kernel to use, must be an odd number: 3(recommended), 5, 7. 0 means no blindspot.

Default: 0

-bp, --back-projection <back_projection>

Back projection operator, can be: ‘tpsf’ (transposed PSF = classic) or ‘wb’ (Wiener-Butterworth = accelerated)

Default: tpsf
Options: tpsf | wb

-wbo, --wb-order <wb_order>

Wiener-Butterworth order parameter, a higher n makes the filter transition slope closer to a hard cutoff, causing the ringing artifacts in the spatial domain.In contrast, a lower order n makes the transition slope gentler and sacrifice some spectral amplitude at spatial frequencies close to the cutoff.

Default: 5

-obj, --objective <objective>

Microscope objective to use for computing psf, can be: nikon16x08na, olympus20x10na, or path to file

Default: nikon16x08na

-na, --num-ape <num_ape>: Overrides NA value for objective.

-dxy, --dxy <dxy>

Voxel size along x and y in microns

Default: 0.485

-dz, --dz <dz>

Voxel size along z in microns

Default: 1.94

-sxy, --xy-size <xy_size>

PSF size along xy in voxels

Default: 31

-sz, --z-size <z_size>

PSF size along z in voxels

Default: 31

-sp, --show-psf

Show point spread function (PSF) with napari

Default: False

-sc, --scaling <scaling>

Scales input image along the three axis: sz,sy,sx (numpy order). For example: 2,1,1 upscales along z by a factor 2

Default: 1,1,1

Arguments

INPUT_PATHS: Optional argument(s)

deskew 

Denoises input image using butterworth filter, parameters are estimated automatically: using noise2self j-invariant cross-validation loss.

deskew [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-c, --channels <channels>: list of channels, all channels when ommited.

-d, --devices <devices>

Sets the CUDA devices id, e.g. 0,1,2 or ‘all’

Default: all

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-ts, --tilesize <tilesize>

Tile size for tiled computation

Default: 320

Arguments

INPUT_PATHS: Optional argument(s)

deskew 

Deskews all or selected channels of a dataset.

deskew [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-c, --channels <channels>: list of channels, all channels when ommited.

-d, --devices <devices>

Sets the CUDA devices id, e.g. 0,1,2 or ‘all’

Default: all

-m, --mode <mode>

Deskew algorithm

Default: yang
Options: yang | classic

-xx, --delta-x <delta_x>: Pixel size of the camera

-zz, --delta-z <delta_z>: Scanning step (stage or galvo scanning step, not the same as the distance between the slices)

-a, --angle <angle>: Incident angle of the light sheet, angle between the light sheet and the optical axis in degrees

-fl, --flips <flips>: Flips image to deskew in the opposite orientation (True for view 0 and False for view 1)

-co, --camera-orientation <camera_orientation>

Camera orientation correction expressed as a number of 90 deg rotations to be performed per 2D image in stack – if required.

Default: 0

-za, --depth-axis <depth_axis>

Depth axis.

Default: 0

-xa, --lateral-axis <lateral_axis>

Lateral axis.

Default: 1

-p, --padding: Pads output image to fit deskwed results.

Arguments

INPUT_PATHS: Optional argument(s)

fuse 

Fuses the views of a multi-view light-sheet microscope dataset (available: simview and mvsols)

fuse [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-c, --channels <channels>: list of channels, all channels when ommited.

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-d, --devices <devices>

Sets the CUDA devices id, e.g. 0,1,2 or ‘all’

Default: all

-m, --microscope <microscope>

Microscope objective to use for computing psf, can be: simview or mvsols

Default: simview

-eq, --equalise, -neq, --no-equalise

Equalise intensity of views before fusion, or not.

Default: True

-eqm, --equalisemode <equalisemode>

Equalisation modes: compute correction ratios only for first time point: ‘first’ or for all time points: ‘all’.

Default: first
Options: first | all

-zl, --zerolevel <zerolevel>

‘zero-level’ i.e. the pixel values in the restoration (to be substracted)

Default: 0

-ch, --cliphigh <cliphigh>

Clips voxel values above the given value, if zero no clipping is done

Default: 0

-f, --fusion <fusion>

Fusion mode, can be: ‘tg’ or ‘dct’.

Default: tg
Options: tg | dct

-fbs, --fusion_bias_strength <fusion_bias_strength>

Fusion bias strength for illumination and detection ‘fbs_i fbs_d’, set to ‘0 0’) if fusing a cropped region

Default: 0.5,0.02

-dhs, --dehaze_size <dehaze_size>

Filter size (scale) for dehazing the final regsitered and fused image to reduce effect of scattered and out-of-focus light. Set to zero to deactivate.

Default: 65

-ddt, --dark-denoise-threshold <dark_denoise_threshold>

Threshold for denoises the dark pixels of the image – helps increase compression ratio. Set to zero to deactivate.

Default: 0

-zpa, --zpadapodise <zpadapodise>

Pads and apodises the views along z before fusion: ‘pad apo’, where pad is a padding length, and apo is apodisation length, both in voxels. If pad=apo, no original voxel is modified and only added voxels are apodised.

Default: 8,96

-lr, --loadreg

Turn on to load the registration parameters from a previous run

Default: False

-mf, --model-filename <model_filename>

Model filename to load or save registration model list

Default: registration_models.txt

-wri, --warpregiter <warpregiter>

Number of iterations for warp registration (if applicable).

Default: 4

-mc, --minconfidence <minconfidence>

Minimal confidence for registration parameters, if below that level the registration parameters for previous time points is used.

Default: 0.3

-md, --maxchange <maxchange>

Maximal change in registration parameters, if above that level the registration parameters for previous time points is used.

Default: 16

-ref, --regedgefilter

Use this flag to apply an edge filter to help registration.

Default: False

-mp, --maxproj, -nmp, --no-maxproj

Registers using only the maximum intensity projection from each stack.

Default: True

-hd, --hugedataset

Use this flag to indicate that the the dataset is _huge_ and that memory allocation should be optimised at the detriment of processing speed.

Default: False

-p, --pad: Use this flag to pad views according to the registration models.

-wth, --white-top-hat-size <white_top_hat_size>: Area opening value after down sampling for white top hat transform transform. Larger values will keep larger components. Recommended value of 1e5.

-wths, --white-top-hat-sampling <white_top_hat_sampling>: Down sampling size to compute the area opening

-rb, --remove-beads: Use this flag to remove beads before equalizing and fusing

-eqr, --equalisation-ratios <equalisation_ratios>: Manually set equalisation ratios

Arguments

INPUT_PATHS: Optional argument(s)

info 

Prints out extensive information about dataset.

info [OPTIONS] [INPUT_PATHS]...

Arguments

INPUT_PATHS: Optional argument(s)

info 

Executes a generic function in multiples gpus using dask and cupy.

info [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-c, --channels <channels>: list of channels, all channels when ommited.

-d, --devices <devices>

Sets the CUDA devices id, e.g. 0,1,2 or ‘all’

Default: all

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-ts, --tilesize <tilesize>: Tile size for tiled computation

-a, --args <args>: Function arguments, it must be used multiple times for multiple arguments. Example: -a sigma=1,2,3 -a pad=constant

-f, --func-name <func_name>: Required Function to be called, arguments should be provided as keyword arguments on the cli.

-pkg, --pkg-import <pkg_import>: Required Package to be imported for function usage. For example, cupyx.scipy.ndimage when using gaussian_filter.

Arguments

INPUT_PATHS: Optional argument(s)

info 

Computes histogram of selected channel.

info [OPTIONS] [INPUT_PATHS]...

Options

-c, --channels <channels>: list of channels, all channels when ommited.

-d, --device <device>

Selects the CUDA device by id, starting from 0.

Default: 0

-o, --output-directory <output_directory>

Default: histogram

-m, --minimum-count <minimum_count>

Minimum count on the histogram used to select upper limit, values lower than this are not considered.

Default: 5

-M, --maximum-count <maximum_count>: Maximum count to clip histogram and improve visualization.

Arguments

INPUT_PATHS: Optional argument(s)

projrender 

Renders datatset using 2D projections.

projrender [OPTIONS] [INPUT_PATHS]...

Options

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-c, --channels <channels>: list of channels, all channels when ommited.

-d, --devices <devices>

Sets the CUDA devices id, e.g. 0,1,2 or ‘all’

Default: all

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output_path <output_path>: Output folder to store rendered PNGs. Default is: frames/<channel_name>

-ax, --axis <axis>

Sets the projection axis: 0->Z, 1->Y, 2->X

Default: 0

-di, --dir <dir>

Sets the projection direction: -1 -> top to bottom, +1 -> bottom to top.

Default: -1

-m, --mode <mode>

Sets the projection mode: ‘max’: classic max projection, ‘colormax’: color max projection, i.e. color codes for depth, ‘maxcolor’ same as colormax but first does depth-coding by color and then max projects (acheives some level of transparency).

Default: colormax
Options: max | maxcolor | colormax

-cl, --clim <clim>: Sets the contrast limits, i.e. -cl 0,1000 sets the contrast limits to [0,1000]

-at, --attenuation <attenuation>

Sets the projection attenuation coefficient, should be within [0, 1] ideally close to 0. Larger values mean more attenuation.

Default: 0.1

-g, --gamma <gamma>

Sets the gamma coefficient pre-applied to the raw voxel values (before projection or any subsequent processing).

Default: 1.0

-dl, --dlim <dlim>: Sets the depth limits. Depth limits. For example, a value of (0.1, 0.7) means that the colormap start at a normalised depth of 0.1, and ends at a normalised depth of 0.7, other values are clipped. Only used for colormax mode.

-cm, --colormap <colormap>: sets colormap, e.g. viridis, gray, magma, plasma, inferno. Use a rainbow colormap such as turbo, bmy, or rainbow (recommended) for color-coded depth modes.

-cg, --rgbgamma <rgbgamma>

Gamma correction applied to the resulting RGB image. Usefull to brighten image

Default: 1.0

-t, --transparency

Enables transparency output when possible. Good for rendering on white (e.g. on paper).

Default: False

-lsi, --legend-size <legend_size>

Multiplicative factor to control size of legend. If 0, no legend is generated.

Default: 1.0

-lsc, --legend-scale <legend_scale>

Float that gives the scale in some unit of each voxel (along the projection direction). Only in color projection modes.

Default: 1.0

-lt, --legend-title <legend_title>

Title for the color-coded depth legend.

Default: color-coded depth (voxels)

-ltc, --legend-title-color <legend_title_color>

Legend title color as a tuple of normalised floats: R, G, B, A (values between 0 and 1).

Default: 1,1,1,1

-lp, --legend-position <legend_position>

Position of the legend in pixels in natural order: x,y. Can also be a string: bottom_left, bottom_right, top_left, or top_right.

Default: bottom_left

-la, --legend-alpha <legend_alpha>

Transparency for legend (1 means opaque, 0 means completely transparent)

Default: 1

Arguments

INPUT_PATHS: Optional argument(s)

stabilize 

Segment cells of a combination of multiple detection channels and extract features of each segment from the feature channels.

stabilize [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-d, --devices <devices>

Sets the CUDA devices id, e.g. 0,1,2 or ‘all’

Default: all

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-dc, --detection-channels <detection_channels>: list of channels used to detect cells.

-fc, --features-channels <features_channels>: list of channels for cell features extraction.

-oc, --out-channel <out_channel>

Output channel name.

Default: Segments

-z, --z-scale <z_scale>: Anisotropy over z axis.

-a, --area-threshold <area_threshold>

Parameter for cell detection, a smaller values will detect fewer segments.

Default: 10000.0

-m, --minimum-area <minimum_area>: Minimum area (sum of pixels) per segment.

-h, --h-minima <h_minima>

Parameter to adjust the number of segments, smaller results in more segments.

Default: 1

-cmp, --compactness <compactness>

Cell compactness (convexity) penalization, it penalizes non-convex shapes.

Default: 0

-g, --gamma <gamma>

Gamma parameter to equalize (exponent) the image intensities.

Default: 1.0

-e, --use-edt, -ne

Use Euclidean Distance Transform (EDT) or image intensity for segmentation.

Default: True

Arguments

INPUT_PATHS: Optional argument(s)

speedtest 

Estimates storage medium speed.

speedtest [OPTIONS]

stabilize 

Stabilises dataset against translations across time.

stabilize [OPTIONS] [INPUT_PATHS]...

Options

-l, --clevel <clevel>

Compression level

Default: 3

-z, --codec <codec>

Compression codec: ‘zstd‘, ‘blosclz’, ‘lz4’, ‘lz4hc’, ‘zlib’ or ‘snappy’

Default: zstd

-chk, --chunks <chunks>: Dataset chunks dimensions, e.g. (1, 126, 512, 512).

-st, --store <store>

Zarr store: ‘dir’, ‘ndir’, or ‘zip’

Default: dir

-w, --overwrite

Forces overwrite of output

Default: False

-o, --output-path <output_path>: Dataset output path.

-c, --channels <channels>: list of channels, all channels when ommited.

-rc, --reference-channel <reference_channel>: Reference channel for single stabilization model computation.

-wk, --workers <workers>

Number of worker threads to spawn. Negative numbers n correspond to: number_of _cores / |n|

Default: -4

-d, --device <device>

Selects the CUDA device by id, starting from 0.

Default: 0

-mr, --maxrange <maxrange>

Maximal distance, in time points, between pairs of images to registrate.

Default: 7

-mc, --minconfidence <minconfidence>

Minimal confidence for registration parameters, if below that level the registration parameters for previous time points is used.

Default: 0.5

--com, --no-com

Enable center of mass fallback when standard registration fails.

Default: False

-q, --quantile <quantile>

Quantile to cut-off background in center-of-mass calculation.

Default: 0.5

-t, --tolerance <tolerance>

Tolerance for linear solver.

Default: 1e-07

-oe, --ordererror <ordererror>

Order for linear solver error term.

Default: 2.0

-or, --orderreg <orderreg>

Order for linear solver regularisation term.

Default: 1.0

-or, --alphareg <alphareg>

Multiplicative coefficient for regularisation term.

Default: 0.0001

-rs, --pcsigma <pcsigma>

Sigma for Gaussian smoothing of phase correlogram, zero to disable.

Default: 2

-ds, --dsigma <dsigma>

Sigma for Gaussian smoothing (crude denoising) of input images, zero to disable.

Default: 1.5

-lc, --logcomp <logcomp>

Applies the function log1p to the images to compress high-intensities (usefull when very (too) bright structures are present in the images, such as beads.

Default: True

-ef, --edgefilter

Applies sobel edge filter to input images.

Default: False

-dt, --detrend

Remove linear trend from stabilization result

Default: False

-mp, --maxproj, -nmp, --no-maxproj

Registers using only the maximum intensity projection from each stack.

Default: True

-mi, --model-input-path <model_input_path>: Path to pre-computed model for image registration

-mo, --model-output-path <model_output_path>

Output path for computed registration model

Default: stabilization_model.json

-wkb, --workersbackend <workersbackend>

What backend to spawn workers with, can be ‘loky’ (multi-process) or ‘threading’ (multi-thread)

Default: threading

-d, --device <device>

Sets the CUDA devices id, e.g. 0,1,2

Default: 0

Arguments

INPUT_PATHS: Optional argument(s)

tiff 

Exports dataset as TIFF file(s).

tiff [OPTIONS] [INPUT_PATHS]...

Options

-c, --channels <channels>: list of channels, all channels when ommited.

-s, --slicing <slicing>: dataset slice (TZYX), e.g. [0:5] (first five stacks) [:,0:100] (cropping in z)

-wk, --workers <workers>

Number of worker threads to spawn. Negative numbers n correspond to: number_of _cores / |n|

Default: -4

-o, --output-path <output_path>

-w, --overwrite

to force overwrite of target

Default: False

-p, --project <project>: max projection over given an spatial axis (0->Z, 1->Y, 2->X)

--split: Splits dataset along first dimension, be carefull, if you slice to a single time point this will split along z!

-l, --clevel <clevel>

Compression level, 0 means no compression, max is 9

Default: 0

-wkb, --workersbackend <workersbackend>

What backend to spawn workers with, can be ‘loky’ (multi-process) or ‘threading’ (multi-thread)

Default: threading

Arguments

INPUT_PATHS: Optional argument(s)

view 

Views dataset using napari (napari.org)

view [OPTIONS] [INPUT_PATHS]...

Options

-c, --channels <channels>: list of channels, all channels when ommited.

-d, --downscale <downscale>

Downscale value to speedup visualization

Default: 1

-cl, --clim <clim>

Sets the contrast limits, i.e. -cl 0,1000 sets the contrast limits to [0,1000]

Default: 0,512

-cm, --colormap <colormap>

sets colormap, e.g. viridis, gray, magma, plasma, inferno

Default: magma

-ws, --windowsize <windowsize>

Sets the napari window size. i.e. -ws 400 sets the window to 400x400

Default: 1536

-po, --projectionsonly

To view only the projections, if present.

Default: False

-vo, --volumeonly

To view only the volumetric data.

Default: False

-q, --quiet: Quiet mode. Doesn’t display GUI.

-l, --labels <labels>: Channels to be displayed as labels layer

Arguments

INPUT_PATHS: Optional argument(s)