Conversion

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.

Tip: Named-config chaining

Prefix any command with with_config NAME to use a saved config profile:

eubi with_config hpc to_zarr /data/input /data/output --ome_zarr_version 0.5

to_zarr — Convert image data to OME-Zarr format

Usage:

eubi to_zarr INPUT_PATH [OPTIONS]
eubi with_config NAME to_zarr INPUT_PATH [OPTIONS]

Required arguments

--input_path

Type:  str or Path

Default:  required

File path, directory, or table (.csv/.tsv/.xlsx) of paths.

eubi to_zarr /data/input /data/output

CLI-only options

--output_path

Type:  str or Path or None

Default:  —

Destination directory. Required unless input_path is a table that already contains an output_path column.

eubi to_zarr /data/input /data/output

--includes

Type:  str or None

Default:  —

Comma-separated filename patterns to include (glob-style).

# Include only files whose name contains "EMPIAR"
eubi to_zarr /data/input /data/output --includes "EMPIAR"

# Multiple patterns — comma-separated, no spaces around commas
eubi to_zarr /data/input /data/output --includes "EMPIAR,scan_001,confocal"

--excludes

Type:  str or None

Default:  —

Comma-separated filename patterns to exclude (glob-style).

# Exclude all files in a subdirectory named 'backup'
eubi to_zarr /data/input /data/output --excludes "backup"

# Exclude multiple patterns at once
eubi to_zarr /data/input /data/output --excludes "backup,temp,preview"

--plan

Type:  AggregativePlan or None

Default:  —

Pre-computed AggregativePlan from validate_aggregative().

# Step 1 — validate without converting to inspect the plan
eubi validate_aggregative /data/input /data/output --concatenation_axes c --channel_tag raw,mask

# Step 2 — pass the plan object to skip re-planning on the actual run
eubi to_zarr /data/input /data/output --concatenation_axes c --channel_tag raw,mask --plan <plan>

Cluster overrides

--on_local_cluster

Type:  boolean flag

Default:  False

Valid values:  --on_local_cluster to enable  ·  --on_local_cluster False to disable

Use a Dask LocalCluster.

eubi to_zarr /data/input /data/output --on_local_cluster

--on_slurm

Type:  boolean flag

Default:  False

Valid values:  --on_slurm to enable  ·  --on_slurm False to disable

Submit jobs to a SLURM cluster.

# Submit all file workers to SLURM
eubi to_zarr /data/input /data/output --on_slurm --slurm_account myaccount --slurm_partition gpu

--use_threading

Type:  boolean flag

Default:  False

Valid values:  --use_threading to enable  ·  --use_threading False to disable

Use a ThreadPool instead of a ProcessPool.

eubi to_zarr /data/input /data/output --use_threading

--max_workers

Type:  int

Default:  4

Valid values:  ≥ 1, ≤ 256

Override the configured max_workers for this run.

eubi to_zarr /data/input /data/output --max_workers 8

--queue_size

Type:  int

Default:  4

Valid values:  ≥ 1, ≤ 4096

Internal write-queue depth per worker.

eubi to_zarr /data/input /data/output --queue_size 8

--region_size_mb

Type:  int

Default:  256

Valid values:  > 0

Region size in MB for spatial partitioning.

eubi to_zarr /data/input /data/output --region_size_mb 512

--max_concurrency

Type:  int

Default:  4

Valid values:  ≥ 1

TensorStore write concurrency per worker.

eubi to_zarr /data/input /data/output --max_concurrency 8

--max_concurrent_scenes

Type:  int

Default:  1

Valid values:  ≥ 1

Parallel scenes per file (default 1).

eubi to_zarr /data/input /data/output --max_concurrent_scenes 2

--memory_per_worker

Type:  str

Default:  3GB

Memory limit for SLURM / LocalCluster workers.

eubi to_zarr /data/input /data/output --memory_per_worker 8GB

--tensorstore_data_copy_concurrency

Type:  int

Default:  4

Valid values:  ≥ 1

TensorStore internal copy threads.

eubi to_zarr /data/input /data/output --tensorstore_data_copy_concurrency 8

--max_retries

Type:  int

Default:  10

Valid values:  ≥ 0, ≤ 100

Override the configured max_retries.

eubi to_zarr /data/input /data/output --max_retries 3

--bf_read_concurrency

Type:  int or None

Default:  4

Valid values:  ≥ 1

—

--bf_tile_size_mb

Type:  float

Default:  512.0

Valid values:  > 0.0

—

--jvm_memory

Type:  str or None

Default:  1g

—

--slurm_time

Type:  str

Default:  24:00:00

SLURM wall-clock limit, e.g. '24:00:00'.

eubi to_zarr /data/input /data/output --on_slurm --slurm_time 48:00:00

--slurm_account

Type:  str or None

Default:  —

SLURM account name.

eubi to_zarr /data/input /data/output --on_slurm --slurm_account myaccount

--slurm_partition

Type:  str or None

Default:  —

SLURM partition / queue.

eubi to_zarr /data/input /data/output --on_slurm --slurm_partition gpu

--slurm_worker_timeout

Type:  int

Default:  300

Valid values:  > 0

Seconds to wait for SLURM workers to start.

eubi to_zarr /data/input /data/output --on_slurm --slurm_worker_timeout 600

--slurm_sif_path

Type:  str or None

Default:  —

Path to an Apptainer/Singularity .sif image to run SLURM workers inside (optional).

eubi to_zarr /data/input /data/output --on_slurm --slurm_sif_path /apps/eubi.sif

--max_concurrent_downscale_layers

Type:  int

Default:  3

Valid values:  > 0

How many pyramid levels are downscaled in parallel per file (default 1 = sequential, lowest memory).

eubi to_zarr /data/input /data/output --max_concurrent_downscale_layers 2

Conversion overrides

--verbose

Type:  boolean flag

Default:  False

Valid values:  --verbose to enable  ·  --verbose False to disable

Log verbose per-chunk progress output.

eubi to_zarr /data/input /data/output --verbose

--ome_zarr_version

Type:  str or None

Default:  —

OME-Zarr (NGFF) version to write: 0.4 (backed by Zarr v2) or 0.5 (backed by Zarr v3, which enables sharding). This is the preferred control and supersedes zarr_format — the underlying zarr container format is derived from it.

# Write OME-Zarr 0.4 (Zarr v2, the default)
eubi to_zarr /data/input /data/output --ome_zarr_version 0.4

# Write OME-Zarr 0.5 (Zarr v3 — required for sharding)
eubi to_zarr /data/input /data/output --ome_zarr_version 0.5

--zarr_format

Type:  2 or 3

Default:  2

Deprecated — use ome_zarr_version instead. Zarr container version: 2 = OME-Zarr 0.4 (classic chunk-based); 3 = OME-Zarr 0.5 (sharding support).

eubi to_zarr /data/input /data/output --zarr_format 3

--skip_dask

Type:  boolean flag

Default:  False

Valid values:  --skip_dask to enable  ·  --skip_dask False to disable

Read TIFF files via zarr's native aszarr backend instead of dask. Faster for large TIFFs; ignored for non-TIFF formats.

eubi to_zarr /data/input /data/output --skip_dask

--auto_chunk

Type:  boolean flag

Default:  True

Valid values:  --auto_chunk to enable  ·  --auto_chunk False to disable

Auto-compute chunk shape to approximate target_chunk_mb. When False, the manual *_chunk values below are used.

eubi to_zarr /data/input /data/output --auto_chunk False --z_chunk 64 --y_chunk 256 --x_chunk 256

--target_chunk_mb

Type:  float

Default:  1.0

Valid values:  > 0.0

Target uncompressed chunk size in MB when auto_chunk=True.

eubi to_zarr /data/input /data/output --target_chunk_mb 4.0

--time_chunk

Type:  int

Default:  1

Valid values:  ≥ 1

Chunk size along the time axis. Applies only when auto_chunk=False.

eubi to_zarr /data/input /data/output --auto_chunk False --time_chunk 1

--channel_chunk

Type:  int

Default:  1

Valid values:  ≥ 1

Chunk size along the channel axis. Applies only when auto_chunk=False.

eubi to_zarr /data/input /data/output --auto_chunk False --channel_chunk 1

--z_chunk

Type:  int

Default:  96

Valid values:  ≥ 1

Chunk size along the z axis. Applies only when auto_chunk=False.

eubi to_zarr /data/input /data/output --auto_chunk False --z_chunk 64

--y_chunk

Type:  int

Default:  96

Valid values:  ≥ 1

Chunk size along the y axis. Applies only when auto_chunk=False.

eubi to_zarr /data/input /data/output --auto_chunk False --y_chunk 256

--x_chunk

Type:  int

Default:  96

Valid values:  ≥ 1

Chunk size along the x axis. Applies only when auto_chunk=False.

eubi to_zarr /data/input /data/output --auto_chunk False --x_chunk 256

--time_shard_coef

Type:  int

Default:  1

Valid values:  ≥ 1

Shard size = chunk × coef for the time axis. Zarr v3 only — ignored for v2.

eubi to_zarr /data/input /data/output --ome_zarr_version 0.5 --time_shard_coef 1

--channel_shard_coef

Type:  int

Default:  1

Valid values:  ≥ 1

Shard size = chunk × coef for the channel axis. Zarr v3 only — ignored for v2.

eubi to_zarr /data/input /data/output --ome_zarr_version 0.5 --channel_shard_coef 1

--z_shard_coef

Type:  int

Default:  3

Valid values:  ≥ 1

Shard size = chunk × coef for the z axis. Zarr v3 only — ignored for v2.

eubi to_zarr /data/input /data/output --ome_zarr_version 0.5 --z_shard_coef 5

--y_shard_coef

Type:  int

Default:  3

Valid values:  ≥ 1

Shard size = chunk × coef for the y axis. Zarr v3 only — ignored for v2.

eubi to_zarr /data/input /data/output --ome_zarr_version 0.5 --y_shard_coef 5

--x_shard_coef

Type:  int

Default:  3

Valid values:  ≥ 1

Shard size = chunk × coef for the x axis. Zarr v3 only — ignored for v2.

eubi to_zarr /data/input /data/output --ome_zarr_version 0.5 --x_shard_coef 5

--time_range

Type:  Any or None

Default:  —

Crop the time axis before writing. Pass as a "start,stop" string (e.g. "0,10" to keep frames 0–9).

eubi to_zarr /data/input /data/output --time_range "0,10"

--channel_range

Type:  Any or None

Default:  —

Crop the channel axis. Same format as time_range, e.g. "0,2" keeps the first two channels.

eubi to_zarr /data/input /data/output --channel_range "0,2"

--z_range

Type:  Any or None

Default:  —

Crop the z axis. Same format as time_range, e.g. "5,50" keeps z-slices 5–49.

eubi to_zarr /data/input /data/output --z_range "5,50"

--y_range

Type:  Any or None

Default:  —

Crop the y axis. Same format as time_range.

eubi to_zarr /data/input /data/output --y_range "0,512"

--x_range

Type:  Any or None

Default:  —

Crop the x axis. Same format as time_range.

eubi to_zarr /data/input /data/output --x_range "0,512"

--dimension_order

Type:  str

Default:  tczyx

Axis order string for the output array (default tczyx).

--compressor

Type:  str or None

Default:  blosc

Valid values:  v2: blosc, bz2, gzip, none, zstd; v3: blosc, crc32ccodec, gzip, none, sharding, zstd

Compression codec.

eubi to_zarr /data/input /data/output --compressor zstd

--compressor_params

Type:  dict

Default:  (auto)

Codec-specific parameters dict. When omitted, sensible defaults are used (e.g. for blosc: {'cname': 'lz4', 'clevel': 5, 'shuffle': 1}).

eubi to_zarr /data/input /data/output --compressor blosc --compressor_params '{"cname": "lz4", "clevel": 9}'

--overwrite

Type:  boolean flag

Default:  False

Valid values:  --overwrite to enable  ·  --overwrite False to disable

Overwrite existing output zarr if it already exists.

eubi to_zarr /data/input /data/output --overwrite

--override_channel_names

Type:  boolean flag

Default:  False

Valid values:  --override_channel_names to enable  ·  --override_channel_names False to disable

Replace output channel labels with the channel_tag values. For aggregative conversions with a tuple channel_tag only.

eubi to_zarr /data/input /data/output --concatenation_axes c --channel_tag raw,mask --override_channel_names

--channel_intensity_limits

Type:  from_dtype or from_array or auto

Default:  from_dtype

Valid values:  from_dtype · from_array · auto

Strategy for OMERO display-window limits.

eubi to_zarr /data/input /data/output --channel_intensity_limits from_array

--metadata_reader

Type:  str

Default:  bfio

Valid values:  bfio · bioformats

Backend used to read OME-XML pixel metadata.

eubi to_zarr /data/input /data/output --metadata_reader bioformats

--save_omexml

Type:  boolean flag

Default:  True

Valid values:  --save_omexml to enable  ·  --save_omexml False to disable

Write a companion OME-XML sidecar file alongside the zarr.

eubi to_zarr /data/input /data/output --save_omexml False

--squeeze

Type:  boolean flag

Default:  True

Valid values:  --squeeze to enable  ·  --squeeze False to disable

Remove length-1 dimensions before writing.

eubi to_zarr /data/input /data/output --squeeze False

--dtype

Type:  str or None

Default:  auto

auto preserves the source dtype; pass any NumPy dtype string (e.g. uint16, float32) to cast on write.

eubi to_zarr /data/input /data/output --dtype uint8

Downscale overrides

--time_scale_factor

Type:  int

Default:  1

Valid values:  ≥ 1

Downscale factor for the time axis per pyramid level.

eubi to_zarr /data/input /data/output --time_scale_factor 1

--channel_scale_factor

Type:  int

Default:  1

Valid values:  ≥ 1

Downscale factor for the channel axis.

eubi to_zarr /data/input /data/output --channel_scale_factor 1

--z_scale_factor

Type:  int

Default:  2

Valid values:  ≥ 1

Downscale factor for the z axis.

# Isotropic downscaling on all spatial axes
eubi to_zarr /data/input /data/output --z_scale_factor 2 --y_scale_factor 2 --x_scale_factor 2

# Anisotropic — skip z downscaling for thick sections
eubi to_zarr /data/input /data/output --z_scale_factor 1 --y_scale_factor 2 --x_scale_factor 2

--y_scale_factor

Type:  int

Default:  2

Valid values:  ≥ 1

Downscale factor for the y axis.

eubi to_zarr /data/input /data/output --y_scale_factor 2

--x_scale_factor

Type:  int

Default:  2

Valid values:  ≥ 1

Downscale factor for the x axis.

eubi to_zarr /data/input /data/output --x_scale_factor 2

--n_layers

Type:  int or None

Default:  —

Number of pyramid levels (None = auto).

eubi to_zarr /data/input /data/output --n_layers 5

--min_dimension_size

Type:  int

Default:  64

Valid values:  > 0

Stop downscaling when smallest dimension reaches this size.

eubi to_zarr /data/input /data/output --min_dimension_size 32

--downscale_method

Type:  simple or mean or median or min or max or mode

Default:  simple

Valid values:  simple · mean · median · min · max · mode

simple = stride/nearest (fastest). mean / median / min / max / mode = aggregation methods passed to TensorStore.

# Use mean aggregation (recommended for fluorescence images)
eubi to_zarr /data/input /data/output --downscale_method mean

# Use nearest-neighbour striding (fastest, recommended for label images)
eubi to_zarr /data/input /data/output --downscale_method simple

--keep_existing_resolutions

Type:  boolean flag

Default:  False

Valid values:  --keep_existing_resolutions to enable  ·  --keep_existing_resolutions False to disable

If the input already carries its own multiscale pyramid (e.g. .ims, .zarr), write each existing resolution level straight to the output OME-Zarr instead of rebuilding the pyramid (default False).

# Copy an .ims / .zarr input's own pyramid levels instead of rebuilding them
eubi to_zarr /data/input /data/output --keep_existing_resolutions

--apply_smart_downscaling

Type:  boolean flag

Default:  False

Valid values:  --apply_smart_downscaling to enable  ·  --apply_smart_downscaling False to disable

Choose per-axis downscale factors automatically from the pixel anisotropy so the pyramid approaches isotropy, instead of using the fixed *_scale_factor values (default False).

# Let EuBI-Bridge pick per-axis factors from the voxel anisotropy
eubi to_zarr /data/input /data/output --apply_smart_downscaling

--time_smart_scale_factor

Type:  int or None

Default:  —

Override the smart-downscaling factor for the time axis (used when apply_smart_downscaling=True).

eubi to_zarr /data/input /data/output --apply_smart_downscaling --time_smart_scale_factor 1

--z_smart_scale_factor

Type:  int or None

Default:  —

Override the smart-downscaling factor for the z axis (used when apply_smart_downscaling=True).

eubi to_zarr /data/input /data/output --apply_smart_downscaling --z_smart_scale_factor 1

--y_smart_scale_factor

Type:  int or None

Default:  —

Override the smart-downscaling factor for the y axis (used when apply_smart_downscaling=True).

eubi to_zarr /data/input /data/output --apply_smart_downscaling --y_smart_scale_factor 2

--x_smart_scale_factor

Type:  int or None

Default:  —

Override the smart-downscaling factor for the x axis (used when apply_smart_downscaling=True).

eubi to_zarr /data/input /data/output --apply_smart_downscaling --x_smart_scale_factor 2

Reader overrides

--as_mosaic

Type:  boolean flag

Default:  False

Valid values:  --as_mosaic to enable  ·  --as_mosaic False to disable

Stitch all mosaic tiles into a single full field-of-view output (instead of one OME-Zarr per tile).

# Stitch all mosaic tiles into a single full field-of-view output
eubi to_zarr /data/input /data/output --as_mosaic

--view_index

Type:  int or str

Default:  0

View(s) to read. Pass an integer, all, or comma-separated integers; each selected view becomes a separate OME-Zarr (named _view{N}) unless --concat_views stacks them along the channel axis.

# Write each view as its own OME-Zarr
eubi to_zarr /data/input /data/output --view_index all

# Concatenate all views along the channel axis into one output
eubi to_zarr /data/input /data/output --view_index all --concat_views

--phase_index

Type:  int

Default:  0

Valid values:  ≥ 0

Phase index.

eubi to_zarr /data/input /data/output --phase_index 1

--illumination_index

Type:  int or str

Default:  0

Illumination(s) to read. Pass an integer, all, or comma-separated integers; each selected illumination becomes a separate OME-Zarr (named _illu{N}) unless --concat_illuminations stacks them along the channel axis.

# Write each illumination as its own OME-Zarr
eubi to_zarr /data/input /data/output --illumination_index all

# Concatenate all illuminations along the channel axis into one output
eubi to_zarr /data/input /data/output --illumination_index all --concat_illuminations

--scene_index

Type:  int or str

Default:  0

Scene / series index to read. Pass an integer for a single scene, all to convert each scene to a separate zarr group, or comma-separated integers (e.g. 0,2,4) for a subset of scenes.

# Convert only scene 2 from a multi-scene file
eubi to_zarr /data/input /data/output --scene_index 2

# Convert every scene to a separate OME-Zarr group
eubi to_zarr /data/input /data/output --scene_index all

# Convert scenes 0, 2 and 4 only
eubi to_zarr /data/input /data/output --scene_index 0,2,4

--rotation_index

Type:  int

Default:  0

Valid values:  ≥ 0

Rotation index.

eubi to_zarr /data/input /data/output --rotation_index 0

--mosaic_tile_index

Type:  int or str or None

Default:  —

Mosaic tile(s) to read when not stitching. Pass an integer, all, or comma-separated integers; each selected tile becomes a separate OME-Zarr (named _tile{N}). Use --as_mosaic instead to stitch tiles into one output. Composes with scene / view / illumination selection (cartesian product).

# Write every tile as its own OME-Zarr (default — each tile separate)
eubi to_zarr /data/input /data/output --mosaic_tile_index all

# Write only tiles 0 and 2 (each as a separate output)
eubi to_zarr /data/input /data/output --mosaic_tile_index 0,2

# Stitch all tiles into one mosaic instead of writing them separately
eubi to_zarr /data/input /data/output --as_mosaic

--sample_index

Type:  int

Default:  0

Valid values:  ≥ 0

Sample index.

eubi to_zarr /data/input /data/output --sample_index 0

--force_bioformats

Type:  boolean flag

Default:  False

Valid values:  --force_bioformats to enable  ·  --force_bioformats False to disable

Force the Java Bio-Formats reader even for formats EuBI-Bridge reads natively (CZI, ND2, LIF, IMS…). Useful as a fallback when a native read fails.

eubi to_zarr /data/input /data/output --force_bioformats

--concat_views

Type:  boolean flag

Default:  False

Valid values:  --concat_views to enable  ·  --concat_views False to disable

When reading multiple views, stack them along the channel axis into one output (cartesian product with existing channels) instead of writing one OME-Zarr per view.

# Stack every view onto the channel axis (cartesian with existing channels)
eubi to_zarr /data/input /data/output --view_index all --concat_views

--concat_illuminations

Type:  boolean flag

Default:  False

Valid values:  --concat_illuminations to enable  ·  --concat_illuminations False to disable

When reading multiple illuminations, stack them along the channel axis into one output (cartesian product with existing channels) instead of writing one OME-Zarr per illumination.

# Stack every illumination onto the channel axis (cartesian with existing channels)
eubi to_zarr /data/input /data/output --illumination_index all --concat_illuminations

Concatenation overrides

--concatenation_axes

Type:  str or int or None

Default:  —

Axes to concatenate across files, e.g. 'tc'. If omitted the config value is used; None means unary conversion.

# Concatenate files along the channel axis
eubi to_zarr /data/input /data/output --concatenation_axes c --channel_tag raw,mask

# Concatenate along both z and channel axes simultaneously
eubi to_zarr /data/input /data/output --concatenation_axes zc --z_tag slices --channel_tag raw,mask

--time_tag

Type:  str or List or None

Default:  —

Filename tag identifying the time axis (aggregative only).

# Three time points identified by substrings in each filename
eubi to_zarr /data/input /data/output --concatenation_axes t --time_tag t001,t002,t003

--channel_tag

Type:  str or List or None

Default:  —

Filename tag identifying the channel axis.

# Two channels — raw fluorescence and segmentation mask
eubi to_zarr /data/input /data/output --concatenation_axes c --channel_tag raw,mask

# Single channel — assign a label without concatenating
eubi to_zarr /data/input /data/output --concatenation_axes c --channel_tag DAPI

--z_tag

Type:  str or List or None

Default:  —

Filename tag identifying the z axis.

# Multiple z-slices acquired as separate files
eubi to_zarr /data/input /data/output --concatenation_axes z --z_tag slice001,slice002,slice003

--y_tag

Type:  str or List or None

Default:  —

Filename tag identifying the y axis.

eubi to_zarr /data/input /data/output --concatenation_axes y --y_tag row_top,row_bottom

--x_tag

Type:  str or List or None

Default:  —

Filename tag identifying the x axis.

eubi to_zarr /data/input /data/output --concatenation_axes x --x_tag col_left,col_right

validate_aggregative — Dry-run an aggregative conversion and print the resource plan

Usage:

eubi validate_aggregative INPUT_PATH [OPTIONS]
eubi with_config NAME validate_aggregative INPUT_PATH [OPTIONS]

Determines output groups and worker allocation without reading any pixel data. Prints a human-readable summary and returns the plan object so it can be passed to :meth:to_zarr to skip re-planning.

Required arguments

--input_path

Type:  str or Path

Default:  required

File path, directory, or table of paths.

eubi validate_aggregative /data/input /data/output --concatenation_axes c --channel_tag raw,mask

CLI-only options

--output_path

Type:  str or Path or None

Default:  —

Destination directory.

eubi validate_aggregative /data/input /data/output --concatenation_axes c --channel_tag raw,mask

--includes

Type:  str or None

Default:  —

Comma-separated filename patterns to include.

# Plan the conversion but only include files matching "scan"
eubi validate_aggregative /data/input /data/output --concatenation_axes c --channel_tag raw,mask --includes "scan"

--excludes

Type:  str or None

Default:  —

Comma-separated filename patterns to exclude.

# Exclude preview files from the plan
eubi validate_aggregative /data/input /data/output --concatenation_axes c --channel_tag raw,mask --excludes "preview"

Cluster overrides

--on_local_cluster

Type:  boolean flag

Default:  False

Valid values:  --on_local_cluster to enable  ·  --on_local_cluster False to disable

Use a Dask LocalCluster backend.

eubi to_zarr /data/input /data/output --on_local_cluster

--on_slurm

Type:  boolean flag

Default:  False

Valid values:  --on_slurm to enable  ·  --on_slurm False to disable

Submit to a SLURM cluster.

# Submit all file workers to SLURM
eubi to_zarr /data/input /data/output --on_slurm --slurm_account myaccount --slurm_partition gpu

--use_threading

Type:  boolean flag

Default:  False

Valid values:  --use_threading to enable  ·  --use_threading False to disable

Use ThreadPool instead of ProcessPool.

eubi to_zarr /data/input /data/output --use_threading

--max_workers

Type:  int

Default:  4

Valid values:  ≥ 1, ≤ 256

Number of parallel file-level worker processes.

eubi to_zarr /data/input /data/output --max_workers 8

--queue_size

Type:  int

Default:  4

Valid values:  ≥ 1, ≤ 4096

Internal write-queue depth per worker.

eubi to_zarr /data/input /data/output --queue_size 8

--region_size_mb

Type:  int

Default:  256

Valid values:  > 0

Region size in MB for spatial partitioning.

eubi to_zarr /data/input /data/output --region_size_mb 512

--max_concurrency

Type:  int

Default:  4

Valid values:  ≥ 1

TensorStore write concurrency per worker.

eubi to_zarr /data/input /data/output --max_concurrency 8

--max_concurrent_scenes

Type:  int

Default:  1

Valid values:  ≥ 1

Parallel scenes per file (default 1).

eubi to_zarr /data/input /data/output --max_concurrent_scenes 2

--memory_per_worker

Type:  str

Default:  3GB

Memory limit for SLURM / LocalCluster workers.

eubi to_zarr /data/input /data/output --memory_per_worker 8GB

--tensorstore_data_copy_concurrency

Type:  int

Default:  4

Valid values:  ≥ 1

TensorStore internal copy threads.

eubi to_zarr /data/input /data/output --tensorstore_data_copy_concurrency 8

--max_retries

Type:  int

Default:  10

Valid values:  ≥ 0, ≤ 100

Retries on a broken worker process.

eubi to_zarr /data/input /data/output --max_retries 3

--bf_read_concurrency

Type:  int or None

Default:  4

Valid values:  ≥ 1

—

--bf_tile_size_mb

Type:  float

Default:  512.0

Valid values:  > 0.0

—

--jvm_memory

Type:  str or None

Default:  1g

—

--slurm_time

Type:  str

Default:  24:00:00

SLURM wall-clock limit, e.g. '24:00:00'.

eubi to_zarr /data/input /data/output --on_slurm --slurm_time 48:00:00

--slurm_account

Type:  str or None

Default:  —

SLURM account name.

eubi to_zarr /data/input /data/output --on_slurm --slurm_account myaccount

--slurm_partition

Type:  str or None

Default:  —

SLURM partition / queue.

eubi to_zarr /data/input /data/output --on_slurm --slurm_partition gpu

--slurm_worker_timeout

Type:  int

Default:  300

Valid values:  > 0

Seconds to wait for SLURM workers to start.

eubi to_zarr /data/input /data/output --on_slurm --slurm_worker_timeout 600

--slurm_sif_path

Type:  str or None

Default:  —

Path to an Apptainer/Singularity .sif image to run SLURM workers inside (optional).

eubi to_zarr /data/input /data/output --on_slurm --slurm_sif_path /apps/eubi.sif

--max_concurrent_downscale_layers

Type:  int

Default:  3

Valid values:  > 0

How many pyramid levels are downscaled in parallel per file (default 1 = sequential, lowest memory).

eubi to_zarr /data/input /data/output --max_concurrent_downscale_layers 2

Reader overrides

--as_mosaic

Type:  boolean flag

Default:  False

Valid values:  --as_mosaic to enable  ·  --as_mosaic False to disable

Stitch all mosaic tiles into a single full field-of-view output (instead of one OME-Zarr per tile).

# Stitch all mosaic tiles into a single full field-of-view output
eubi to_zarr /data/input /data/output --as_mosaic

--view_index

Type:  int or str

Default:  0

View(s) to read. Pass an integer, all, or comma-separated integers; each selected view becomes a separate OME-Zarr (named _view{N}) unless --concat_views stacks them along the channel axis.

# Write each view as its own OME-Zarr
eubi to_zarr /data/input /data/output --view_index all

# Concatenate all views along the channel axis into one output
eubi to_zarr /data/input /data/output --view_index all --concat_views

--phase_index

Type:  int

Default:  0

Valid values:  ≥ 0

Phase index.

eubi to_zarr /data/input /data/output --phase_index 1

--illumination_index

Type:  int or str

Default:  0

Illumination(s) to read. Pass an integer, all, or comma-separated integers; each selected illumination becomes a separate OME-Zarr (named _illu{N}) unless --concat_illuminations stacks them along the channel axis.

# Write each illumination as its own OME-Zarr
eubi to_zarr /data/input /data/output --illumination_index all

# Concatenate all illuminations along the channel axis into one output
eubi to_zarr /data/input /data/output --illumination_index all --concat_illuminations

--scene_index

Type:  int or str

Default:  0

Scene / series index to read. Pass an integer for a single scene, all to convert each scene to a separate zarr group, or comma-separated integers (e.g. 0,2,4) for a subset of scenes.

# Convert only scene 2 from a multi-scene file
eubi to_zarr /data/input /data/output --scene_index 2

# Convert every scene to a separate OME-Zarr group
eubi to_zarr /data/input /data/output --scene_index all

# Convert scenes 0, 2 and 4 only
eubi to_zarr /data/input /data/output --scene_index 0,2,4

--rotation_index

Type:  int

Default:  0

Valid values:  ≥ 0

Rotation index.

eubi to_zarr /data/input /data/output --rotation_index 0

--mosaic_tile_index

Type:  int or str or None

Default:  —

Mosaic tile(s) to read when not stitching. Pass an integer, all, or comma-separated integers; each selected tile becomes a separate OME-Zarr (named _tile{N}). Use --as_mosaic instead to stitch tiles into one output. Composes with scene / view / illumination selection (cartesian product).

# Write every tile as its own OME-Zarr (default — each tile separate)
eubi to_zarr /data/input /data/output --mosaic_tile_index all

# Write only tiles 0 and 2 (each as a separate output)
eubi to_zarr /data/input /data/output --mosaic_tile_index 0,2

# Stitch all tiles into one mosaic instead of writing them separately
eubi to_zarr /data/input /data/output --as_mosaic

--sample_index

Type:  int

Default:  0

Valid values:  ≥ 0

Sample index.

eubi to_zarr /data/input /data/output --sample_index 0

--force_bioformats

Type:  boolean flag

Default:  False

Valid values:  --force_bioformats to enable  ·  --force_bioformats False to disable

Force the Java Bio-Formats reader even for formats EuBI-Bridge reads natively (CZI, ND2, LIF, IMS…). Useful as a fallback when a native read fails.

eubi to_zarr /data/input /data/output --force_bioformats

--concat_views

Type:  boolean flag

Default:  False

Valid values:  --concat_views to enable  ·  --concat_views False to disable

When reading multiple views, stack them along the channel axis into one output (cartesian product with existing channels) instead of writing one OME-Zarr per view.

# Stack every view onto the channel axis (cartesian with existing channels)
eubi to_zarr /data/input /data/output --view_index all --concat_views

--concat_illuminations

Type:  boolean flag

Default:  False

Valid values:  --concat_illuminations to enable  ·  --concat_illuminations False to disable

When reading multiple illuminations, stack them along the channel axis into one output (cartesian product with existing channels) instead of writing one OME-Zarr per illumination.

# Stack every illumination onto the channel axis (cartesian with existing channels)
eubi to_zarr /data/input /data/output --illumination_index all --concat_illuminations

Concatenation overrides

--concatenation_axes

Type:  str or int or None

Default:  —

Axes to concatenate, e.g. 'c'.

# Plan a channel concatenation
eubi validate_aggregative /data/input /data/output --concatenation_axes c --channel_tag raw,mask

# Plan a z + channel concatenation
eubi validate_aggregative /data/input /data/output --concatenation_axes zc --z_tag slices --channel_tag raw,mask

--time_tag

Type:  str or List or None

Default:  —

Filename substring (or tuple of substrings) identifying the time axis.

# Plan concatenation of three time points
eubi validate_aggregative /data/input /data/output --concatenation_axes t --time_tag t001,t002,t003

--channel_tag

Type:  str or List or None

Default:  —

Filename substring (or tuple of substrings) identifying the channel axis.

# Two channels — raw fluorescence and segmentation mask
eubi validate_aggregative /data/input /data/output --concatenation_axes c --channel_tag raw,mask

--z_tag

Type:  str or List or None

Default:  —

Filename substring (or tuple of substrings) identifying the z axis.

# Multiple z-slices acquired as separate files
eubi validate_aggregative /data/input /data/output --concatenation_axes z --z_tag slice001,slice002,slice003

--y_tag

Type:  str or List or None

Default:  —

Filename substring (or tuple of substrings) identifying the y axis.

eubi validate_aggregative /data/input /data/output --concatenation_axes y --y_tag row_top,row_bottom

--x_tag

Type:  str or List or None

Default:  —

Filename substring (or tuple of substrings) identifying the x axis.

eubi validate_aggregative /data/input /data/output --concatenation_axes x --x_tag col_left,col_right