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Click any command card below to expand its full parameter reference.

Info

Note that all cards below are auto-generated from EuBIBridge methods and Pydantic config models. Types, defaults, and valid ranges are extracted directly from the source.

show_pixel_meta — Display pixel-level and channel metadata for all files in input_path

Usage:

eubi show_pixel_meta INPUT_PATH [OPTIONS]
eubi with_config NAME show_pixel_meta INPUT_PATH [OPTIONS]

Required arguments

--input_path

Type:  Path or str

Default:  required

File path or directory.

eubi show_pixel_meta /data/input

Optional arguments

--includes

Type:  str or None

Default:  —

Comma-separated filename patterns to include.

# Show metadata only for files whose name contains "EMPIAR"
eubi show_pixel_meta /data/input --includes "EMPIAR"

# Multiple patterns — comma-separated
eubi show_pixel_meta /data/input --includes "EMPIAR,scan_001,confocal"

--excludes

Type:  str or None

Default:  —

Comma-separated filename patterns to exclude.

# Skip preview files
eubi show_pixel_meta /data/input --excludes "preview"

# Skip multiple patterns
eubi show_pixel_meta /data/input --excludes "preview,temp"

--series

Type:  int

Default:  —

Series / scene index (default: configured scene_index).

eubi show_pixel_meta /data/input --series 2

--output_file

Type:  str

Default:  —

Write output to this path; use .html for HTML output.

# Save as an HTML report you can open in a browser
eubi show_pixel_meta /data/input --output_file report.html

# Save as plain text
eubi show_pixel_meta /data/input --output_file report.txt

update_pixel_meta — Update pixel-scale and unit metadata on existing OME-Zarr files

Usage:

eubi update_pixel_meta INPUT_PATH [OPTIONS]
eubi with_config NAME update_pixel_meta INPUT_PATH [OPTIONS]

Required arguments

--input_path

Type:  Path or str

Default:  required

OME-Zarr path or directory of OME-Zarr files.

eubi update_pixel_meta /data/output

Optional arguments

--includes

Type:  str or None

Default:  —

Comma-separated filename patterns to include.

# Update only files whose name contains "EMPIAR"
eubi update_pixel_meta /data/output --includes "EMPIAR"

--excludes

Type:  str or None

Default:  —

Comma-separated filename patterns to exclude.

# Skip files whose name contains 'backup'
eubi update_pixel_meta /data/output --excludes "backup"

--time_scale

Type:  float

Default:  —

Physical pixel size along the time axis.

eubi update_pixel_meta /data/output --time_scale 1.0 --time_unit second

--z_scale

Type:  float

Default:  —

Physical pixel size along the z axis (e.g. 0.5 for 0.5 µm z-steps).

# Set z-step size and unit together
eubi update_pixel_meta /data/output --z_scale 0.5 --z_unit micrometer

--y_scale

Type:  float

Default:  —

Physical pixel size along the y axis.

eubi update_pixel_meta /data/output --y_scale 0.25 --y_unit micrometer

--x_scale

Type:  float

Default:  —

Physical pixel size along the x axis.

eubi update_pixel_meta /data/output --x_scale 0.25 --x_unit micrometer

--time_unit

Type:  str

Default:  —

Physical unit for the time axis (e.g. second, millisecond).

eubi update_pixel_meta /data/output --time_scale 1.0 --time_unit second

--z_unit

Type:  str

Default:  —

Physical unit for the z axis (e.g. micrometer, nanometer).

eubi update_pixel_meta /data/output --z_scale 0.5 --z_unit micrometer

--y_unit

Type:  str

Default:  —

Physical unit for the y axis.

eubi update_pixel_meta /data/output --y_scale 0.25 --y_unit micrometer

--x_unit

Type:  str

Default:  —

Physical unit for the x axis.

eubi update_pixel_meta /data/output --x_scale 0.25 --x_unit micrometer

--max_workers

Type:  int or None

Default:  —

Number of files to process in parallel.

# Update 8 OME-Zarr stores in parallel
eubi update_pixel_meta /data/output --max_workers 8

update_channel_meta — Update channel label, color, and intensity metadata

Usage:

eubi update_channel_meta INPUT_PATH [OPTIONS]
eubi with_config NAME update_channel_meta INPUT_PATH [OPTIONS]

Required arguments

--input_path

Type:  Path or str

Default:  required

OME-Zarr path or directory of OME-Zarr files.

eubi update_channel_meta /data/output

Optional arguments

--channel_labels

Type:  str

Default:  ""

Index/name pairs, e.g. "0,DAPI;1,GFP".

# Rename channels 0 and 1
eubi update_channel_meta /data/output --channel_labels "0,DAPI;1,GFP"

# Three channels
eubi update_channel_meta /data/output --channel_labels "0,DAPI;1,GFP;2,mCherry"

--channel_colors

Type:  str

Default:  ""

Index/hex pairs, e.g. "0,0000FF;1,00FF00".

# Set display colours in hex (blue DAPI, green GFP)
eubi update_channel_meta /data/output --channel_colors "0,0000FF;1,00FF00"

# Three channels — blue, green, red
eubi update_channel_meta /data/output --channel_colors "0,0000FF;1,00FF00;2,FF0000"

--channel_intensity_limits

Type:  Literal['from_dtype', 'from_array', 'auto']

Default:  from_dtype

'from_dtype' (default), 'from_array', or 'auto'.

# Compute per-channel min/max from the pixel data
eubi update_channel_meta /data/output --channel_intensity_limits from_array

# Let the viewer decide (OMERO-style auto-scaling)
eubi update_channel_meta /data/output --channel_intensity_limits auto

--includes

Type:  str or None

Default:  —

Comma-separated filename patterns to include.

# Update only files whose name contains "EMPIAR"
eubi update_channel_meta /data/output --includes "EMPIAR"

--excludes

Type:  str or None

Default:  —

Comma-separated filename patterns to exclude.

# Skip files whose name contains 'backup'
eubi update_channel_meta /data/output --excludes "backup"

--max_workers

Type:  int or None

Default:  —

Number of files to process in parallel.

# Update 8 OME-Zarr stores in parallel
eubi update_channel_meta /data/output --max_workers 8