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
- flip: Flip images in a dataset
- optimize-registration: Optimize transform based on match filtering
- process-with-config: Process data with YAML-defined functions
- 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
biahub 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" or "input.zarr/*/*/*"
[required]
-t, --transfer-function-dirpath PATH
Path to transfer function .zarr. [required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-j, --num-processes INTEGER Number of parallel processes
-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.
biahub 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" 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.
biahub 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" 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.
biahub 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.
-l, --local Run jobs locally instead of submitting to
SLURM.
-m, --monitor Monitor of submitted SLURM jobs.
-h, --help Show this message and exit.
biahub 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" 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.
biahub 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" 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.
biahub 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" or "input.zarr/*/*/*"
[required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-h, --help Show this message and exit.
biahub 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.
biahub 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" or "input.zarr/*/*/*"
[required]
-o, --output-filepath FILE Path to output file [required]
-h, --help Show this message and exit.
biahub 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" 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.
biahub 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.
biahub 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" 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.
biahub 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" 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.
biahub flip
Flip images in a dataset
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0" or "input.zarr/*/*/*"
[required]
-x Enable the x flag.
-y Enable the y flag.
-h, --help Show this message and exit.
biahub 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.
biahub 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" 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.
biahub reconstruct
Reconstruct a dataset using config
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0" or "input.zarr/*/*/*"
[required]
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-j, --num-processes INTEGER Number of parallel processes
-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.
biahub 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.
biahub 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" 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.
biahub stabilize
Apply stabilization transforms to dataset
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0" 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.
biahub 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" 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.
biahub 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.
biahub virtual-stain
Run VisCy virtual staining
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Paths to input positions, for example:
"input.zarr/0/0/0" or "input.zarr/*/*/*"
[required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
-sb-preprocess, --sbatch-filepath-preprocess FILE
SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-sb-predict, --sbatch-filepath-predict FILE
SBATCH filepath that contains slurm
parameters to overwrite defaults. For
example, '#SBATCH --mem-per-cpu=16G' will
override the default memory per CPU.
-j, --num-processes INTEGER Number of parallel processes
-l, --local Run jobs locally instead of submitting to
SLURM.
-m, --monitor Monitor of submitted SLURM jobs.
--verbose Verbose output.
--path-viscy-env TEXT Conda environment with VisCy installed.
[required]
--preprocess-config-filepath TEXT
Path to the VisCy preprocess config file.
--predict-config-filepath TEXT Path to the VisCy predict config file.
--run-mode [all|preprocess|predict]
Which VisCy stage(s) to run.
-h, --help Show this message and exit.