CLI Reference
This page documents all available biahub command-line tools.
biahub
command-line tools for biahub.
Usage:
Options:
Subcommands
- apply-inv-tf: Apply inverse transfer function to dataset
- characterize-psf: Characterize point spread function (PSF)
- compute-tf: Compute transfer function using PSF
- concatenate: Concatenate datasets (with optional cropping)
- deconvolve: Deconvolve across T and C axes using a PSF
- deskew: Deskew a single position across T and C axes
- estimate-bleaching: Estimate bleaching from raw data
- estimate-crop: Estimate crop region for dual-channel alignment
- estimate-deskew: Routine for estimating deskewing parameters
- estimate-psf: Estimate point spread function from beads
- estimate-registration: Estimate affine transform between timepoints or arms
- estimate-stabilization: Estimate translation matrices for XYZ stabilization
- estimate-stitch: Estimate stitching parameters for positions
- flat-field: Apply flat field correction to selected channels
- flip: Flip images in a dataset
- nf: Nextflow utilities
- optimize-registration: Optimize transform based on match filtering
- process-with-config: Process data with YAML-defined functions
- pyramid: Create pyramid levels for a dataset
- reconstruct: Reconstruct a dataset using config
- register: Apply an affine transformation to a single position
- segment: Segment a position using pretrained model or pipeline
- stabilize: Apply stabilization transforms to dataset
- stitch: Stitch positions in wells of a zarr store
- track: Track objects in 2D/3D time-lapse microscopy
- virtual-stain: Run VisCy virtual staining
apply-inv-tf
Apply inverse transfer function to dataset
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-t, --transfer-function-dirpath PATH
Path to transfer function zarr (not required
for --init).
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
--cluster [slurm|local|debug] Execution cluster: 'slurm' submits to a
Slurm cluster, 'local' runs jobs as
subprocesses on this machine, 'debug' runs
jobs in-process in the foreground.
[default: slurm]
-m, --monitor Monitor of submitted SLURM jobs.
--init Only initialize the output store and exit;
skip per-position processing.
-h, --help Show this message and exit.
characterize-psf
Characterize point spread function (PSF)
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-h, --help Show this message and exit.
compute-tf
Compute transfer function using PSF
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-h, --help Show this message and exit.
concatenate
Concatenate datasets (with optional cropping)
Usage:
Options:
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
--cluster [slurm|local|debug] Execution cluster: 'slurm' submits to a
Slurm cluster, 'local' runs jobs as
subprocesses on this machine, 'debug' runs
jobs in-process in the foreground.
[default: slurm]
-m, --monitor Monitor of submitted SLURM jobs.
--init Only initialize the output store and exit;
skip per-position processing.
--concat-data-paths TEXT Resolve mode: inject these concat_data_paths
into the config and write the resolved
config to -o (a YAML file), then exit.
Repeat the flag once per source store.
-h, --help Show this message and exit.
deconvolve
Deconvolve across T and C axes using a PSF
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-p, --psf-dirpath DIRECTORY Path to psf.zarr [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
deskew
Deskew a single position across T and C axes
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
--cluster [slurm|local|debug] Execution cluster: 'slurm' submits to a
Slurm cluster, 'local' runs jobs as
subprocesses on this machine, 'debug' runs
jobs in-process in the foreground.
[default: slurm]
-m, --monitor Monitor of submitted SLURM jobs.
--init Only initialize the output store and exit;
skip per-position processing.
-h, --help Show this message and exit.
estimate-bleaching
Estimate bleaching from raw data
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-h, --help Show this message and exit.
estimate-crop
Estimate crop region for dual-channel alignment
Usage:
Options:
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-filepath FILE Path to output file [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm parameters
to overwrite defaults. For example, '#SBATCH
--mem-per-cpu=16G' will override the default
memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
--lf-mask-radius FLOAT (Optional) Radius of the circular mask given as
fraction of image width to apply to the phase
channel.
-h, --help Show this message and exit.
estimate-deskew
Routine for estimating deskewing parameters
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-o, --output-filepath FILE Path to output file [required]
-h, --help Show this message and exit.
estimate-psf
Estimate point spread function from beads
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-h, --help Show this message and exit.
estimate-registration
Estimate affine transform between timepoints or arms
Usage:
Options:
-s, --source-position-dirpaths TUPLE
Paths to source positions, for example:
"source.zarr/0/0/0" or "source.zarr/*/*/*"
[required]
-t, --target-position-dirpaths TUPLE
Paths to target positions, for example:
"target.zarr/0/0/0" or "target.zarr/*/*/*"
[required]
-o, --output-filepath FILE Path to output file [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-rt, --registration-target-channel TEXT
Name of the target channel to be used when
registration params are applied. If not
provided, the target channel from the config
file will be used.
-rs, --registration-source-channel TEXT
Name of the source channels to be used when
registration params are applied. May be
passed multiple times. If not provided, the
source channels from the config file will be
used.
-h, --help Show this message and exit.
estimate-stabilization
Estimate translation matrices for XYZ stabilization
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-h, --help Show this message and exit.
estimate-stitch
Estimate stitching parameters for positions
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-o, --output-filepath FILE Path to output file [required]
--fliplr Flip images left-right before stitching
--flipud Flip images up-down before stitching
--flipxy Flip images along the diagonal before
stitching
--pcc-channel-name TEXT Channel name to use for phase cross-
correlation optimization (default: None,
disables optimization)
--pcc-z-index INTEGER Z slice index to use for phase cross-
correlation optimization (default: 0)
--add_offset add the offset to estimated shifts, needed
for OPS experiments
-l, --local Run jobs locally instead of submitting to
SLURM.
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
flat-field
Apply flat field correction to selected channels
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
--cluster [slurm|local|debug] Execution cluster: 'slurm' submits to a
Slurm cluster, 'local' runs jobs as
subprocesses on this machine, 'debug' runs
jobs in-process in the foreground.
[default: slurm]
-m, --monitor Monitor of submitted SLURM jobs.
--init Only initialize the output store and exit;
skip per-position processing.
-h, --help Show this message and exit.
flip
Flip images in a dataset
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-x Enable the x flag.
-y Enable the y flag.
-h, --help Show this message and exit.
nf
Nextflow utilities
Usage:
Options:
Subcommands
- list-positions: List position keys in a plate zarr (one per line, for Nextflow fan-out).
list-positions
List position keys in a plate zarr (one per line, for Nextflow fan-out).
Usage:
Options:
optimize-registration
Optimize transform based on match filtering
Usage:
Options:
-s, --source-position-dirpaths TUPLE
Paths to source positions, for example:
"source.zarr/0/0/0" or "source.zarr/*/*/*"
[required]
-t, --target-position-dirpaths TUPLE
Paths to target positions, for example:
"target.zarr/0/0/0" or "target.zarr/*/*/*"
[required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-filepath FILE Path to output file [required]
-d, --display-viewer Display the registered channels in a napari
viewer
-h, --help Show this message and exit.
process-with-config
Process data with YAML-defined functions
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
pyramid
Create pyramid levels for a dataset
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-lv, --levels INTEGER Total number of resolution levels including
level 0. E.g., levels=4 creates 0, 1, 2, 3.
[default: 4]
-m, --method [stride|median|mode|mean|min|max]
Downsampling method to use. [default: mean]
-h, --help Show this message and exit.
reconstruct
Reconstruct a dataset using config
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
--cluster [slurm|local|debug] Execution cluster: 'slurm' submits to a
Slurm cluster, 'local' runs jobs as
subprocesses on this machine, 'debug' runs
jobs in-process in the foreground.
[default: slurm]
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
register
Apply an affine transformation to a single position
Usage:
Options:
-s, --source-position-dirpaths TUPLE
Paths to source positions, for example:
"source.zarr/0/0/0" or "source.zarr/*/*/*"
[required]
-t, --target-position-dirpaths TUPLE
Paths to target positions, for example:
"target.zarr/0/0/0" or "target.zarr/*/*/*"
[required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-l, --local Run jobs locally instead of submitting to
SLURM.
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
segment
Segment a position using pretrained model or pipeline
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
stabilize
Apply stabilization transforms to dataset
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-c, --config-filepaths TUPLE Paths to YAML configuration files. All must
be existing files with .yml extension.
[required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
stitch
Stitch positions in wells of a zarr store
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-v, --verbose Verbose stitching output. Default is False.
-b, --blending-exponent FLOAT Exponent for blending weights. 0.0 is
average blending, 1.0 is linear blending,
and >1.0 is progressively sharper S-curve
blending.
--debug Run in debug mode
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
track
Track objects in 2D/3D time-lapse microscopy
Usage:
Options:
-o, --output-dirpath DIRECTORY Path to output directory [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-l, --local Run jobs locally instead of submitting to
SLURM.
-h, --help Show this message and exit.
virtual-stain
Run VisCy virtual staining
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb, --sbatch-filepath FILE SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
--cluster [slurm|local|debug] Execution cluster: 'slurm' submits to a
Slurm cluster, 'local' runs jobs as
subprocesses on this machine, 'debug' runs
jobs in-process in the foreground.
[default: slurm]
-m, --monitor Monitor of submitted SLURM jobs.
--init Only initialize the output store and exit;
skip per-position processing.
-h, --help Show this message and exit.