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
- apply-transform: Apply a transform series to positions (registration or stabilization)
- 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-stitch: Estimate stitching parameters for positions
- estimate-transform: Estimate a transform series (registration or stabilization)
- flat-field: Apply flat field correction to selected channels
- flip: Flip images in a dataset
- nf: Nextflow utilities
- process-with-config: Process data with YAML-defined functions
- project: Project a 3D plate to 2D (max, mean, sum or one plane per channel)
- pyramid: Compute multiscale pyramids of a plate's images and label images, in place
- reconstruct: Reconstruct a dataset using config
- segment: Segment a position using pretrained model or pipeline
- stitch: Stitch positions in wells of a zarr store
- substitute-transforms: Replace chosen timepoints of a transforms file with another run's
- 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", "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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-h, --help Show this message and exit.
biahub apply-transform
Apply a transform series to positions (registration or stabilization)
Usage:
Options:
-m, --moving-position-dirpaths TUPLE
Positions of the moving store, for example:
"moving.zarr/0/0/0" or "moving.zarr/*/*/*"
[required]
-r, --reference-position-dirpaths TUPLE
Positions of the reference store, for
example: "reference.zarr/0/0/0" or
"reference.zarr/*/*/*"
-c, --config-filepath FILE Path to YAML configuration file. [required]
-o, --output-dirpath DIRECTORY Path to output directory [required]
--time-indices TEXT Timepoints to write: 'all', one index, or a
comma-separated list (e.g. 0,82,239).
[default: all]
--keep-overhang / --crop-to-overlap
Keep the full reference grid, or crop to the
largest box every transform in the file
covers (one wrong transform can shrink that
box for every timepoint). [default: keep-
overhang]
--interpolation [linear|nearest]
Resampling interpolation. [default: linear]
--ome-zarr-version [0.4|0.5] OME-Zarr version of the output store (0.5
lets --resume track progress). [default:
0.5]
--channels TEXT Moving-store channel to transform (repeat
for several); default: every channel, but
one the reference store also has is copied
unless it is in the file's moving_channels.
-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]
--monitor Monitor of submitted SLURM jobs.
--init Only initialize the output store and exit;
skip per-position processing.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-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", "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.
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", "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.
biahub concatenate
Concatenate datasets (with optional cropping)
Usage:
Options:
-i, --input-position-dirpaths TUPLE
Positions of ONE source store; repeat once
per store, in the order of the config's per-
source entries. For example "-i a.zarr/*/*/*
-i b.zarr/*/*/*" or, for a single position,
"-i a.zarr/A/1/0 -i b.zarr/A/1/0". Overrides
concat_data_paths in the config.
-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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-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", "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.
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", "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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-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", "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.
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", "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.
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", "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.
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", "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.
biahub estimate-transform
Estimate a transform series (registration or stabilization)
Usage:
Options:
-m, --moving-position-dirpaths TUPLE
Positions of the moving store, for example:
"moving.zarr/0/0/0" or "moving.zarr/*/*/*"
[required]
-r, --reference-position-dirpaths TUPLE
Positions of the reference store, for
example: "reference.zarr/0/0/0" or
"reference.zarr/*/*/*"
-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.
--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]
--monitor Monitor of submitted SLURM jobs.
--resume / --no-resume Keep the timepoints an earlier run of this
output already finished and estimate only
the rest (e.g. after jobs hit their time
limit). Refused if the settings or inputs
changed since that run. [default: no-
resume]
--init Only initialize the output store and exit;
skip per-position processing.
--step [estimate|flag|repair|sweep|finalize]
Run one step of a run --init started, in
this process (for Nextflow): estimate ->
flag -> repair / sweep -> finalize.
--timepoints TEXT Timepoints for --step estimate / repair /
sweep, comma-separated (e.g. 5 or 5,6);
default: every timepoint the step has.
-h, --help Show this message and exit.
biahub 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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-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", "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.
biahub nf
Nextflow utilities
Usage:
Options:
Subcommands
- list-positions: List position keys in a plate zarr (one per line, for Nextflow fan-out).
- notify: Post a pipeline notification to Slack, falling back to the terminal.
biahub nf list-positions
List position keys in a plate zarr (one per line, for Nextflow fan-out).
Usage:
Options:
biahub nf notify
Post a pipeline notification to Slack, falling back to the terminal.
Reads the webhook from $BIAHUB_SLACK_WEBHOOK and the operator's member ID
from $BIAHUB_SLACK_ID. With no webhook set, the message is printed rather
than posted.
\b This command ALWAYS exits 0. A failed notification must never fail a reconstruction that has been running for days, so delivery problems are reported on stdout and swallowed.
\b Examples: biahub nf notify --level good --title ":white_check_mark: 2026_07_14 — deskewed" biahub nf notify --level error --ping --title ":x: 2026_07_14 — failed" --detail-file r
Usage:
Options:
--title TEXT One-line summary; should name the dataset.
[required]
--detail TEXT Supporting text, shown in a code fence.
--detail-file FILE Read the detail from a file. Use this for
anything containing quotes, backticks, or
newlines (e.g. a Nextflow error report)
instead of --detail.
--level [info|good|warn|error] Severity, which selects the attachment's
color bar. [default: info]
--ping / --no-ping @-mention $BIAHUB_SLACK_ID. Reserve for
messages needing action.
--slack-id TEXT Member ID override, for testing.
--key TEXT Rate-limit key, e.g. 'run-start'.
--min-interval FLOAT Skip if --key was already sent this
recently, in seconds.
--state-dir DIRECTORY Where --key markers live. Defaults to the
temp dir.
--max-detail INTEGER Character budget for the detail block; the
tail is kept. [default: 2500]
--operator Prepend who launched the run, from the
account database (not Slack).
--log-file FILE Append delivery problems here. Use this when
the caller cannot capture stdout, e.g. a
Nextflow onComplete handler running during
JVM shutdown.
--dry-run Render the payload without posting.
-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", "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.
biahub project
Project a 3D plate to 2D (max, mean, sum or one plane per channel)
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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-h, --help Show this message and exit.
biahub pyramid
Compute multiscale pyramids of a plate's images and label images, in place
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.
--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.
--resume / --no-resume Skip the pyramid regions (one shard of one
level each) an earlier attempt finished,
keyed by the levels and methods; for
retrying an interrupted run. [default: no-
resume]
--levels INTEGER Total number of resolution levels, counting
level 0: 3 adds 2x and 4x levels. [default:
3]
--method [mean|median|mode|min|max|stride]
Downsampling method for the images.
[default: mean]
--label-method [max|stride|mode]
Downsampling method for the label images
under labels/; none invents a label id.
[default: max]
-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", "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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-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", "input.zarr/0/0/[0-9]",
or "input.zarr/*/*/*" [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.
--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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-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", "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.
biahub substitute-transforms
Replace chosen timepoints of a transforms file with another run's
Usage:
Options:
-c, --config-filepath FILE Path to YAML configuration file. [required]
-s, --substitute-filepaths FILE
Transforms file(s) whose timepoints replace
the base's; repeat -s for several, applied
in order. [required]
-o, --output-filepath FILE Path to output file [required]
--positions TEXT Positions (row/col/fov) of a per-position
base that a shared substitute applies to;
repeat for several.
--allow-new Add substitute timepoints the base does not
have instead of refusing them.
-h, --help Show this message and exit.
biahub track
Track objects in 2D/3D time-lapse microscopy
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 Directory to keep the per-FOV Ultrack
databases and the SLURM logs in. If omitted,
each worker builds its database in its own
$TMPDIR and deletes it after export, and the
SLURM logs go to ./slurm_output.
-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.
--input-images-path PATH Pixel-data source filling the first null
input_images path (used by Nextflow). If
omitted, that null path falls back to the -i
input plate.
-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", "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.
--resume / --no-resume Skip the (time, channel) units this position
already finished in an earlier attempt
instead of recomputing the whole position.
For retrying a run that was interrupted,
e.g. by Slurm preemption. Finished units are
keyed by the step's validated settings, so a
settings change recomputes them; a change to
the input data does not, so use a fresh
output store (or --no-resume) after an
upstream step was rerun. [default: no-
resume]
-h, --help Show this message and exit.