diff --git a/conda.yaml b/conda.yaml
index ae44d61a..c8015bf2 100644
--- a/conda.yaml
+++ b/conda.yaml
@@ -19,4 +19,4 @@ dependencies:
   - h5py
   - scipy
   - pip:
-    - cyclopts
+    - cyclopts>=3.0.0
diff --git a/linc_convert/modalities/__init__.py b/linc_convert/modalities/__init__.py
index 98ea30fa..0c741d82 100644
--- a/linc_convert/modalities/__init__.py
+++ b/linc_convert/modalities/__init__.py
@@ -1,5 +1,4 @@
 """Converters for all imaging modalities."""
 
 __all__ = ["df", "lsm", "wk", "psoct"]
-from . import df, lsm, wk, psoct
-
+from . import df, lsm, psoct, wk
diff --git a/linc_convert/modalities/df/multi_slice.py b/linc_convert/modalities/df/multi_slice.py
index e9380f3b..0cedf329 100644
--- a/linc_convert/modalities/df/multi_slice.py
+++ b/linc_convert/modalities/df/multi_slice.py
@@ -22,7 +22,8 @@
 from linc_convert.utils.j2k import WrappedJ2K, get_pixelsize
 from linc_convert.utils.math import ceildiv, floordiv
 from linc_convert.utils.orientation import center_affine, orientation_to_affine
-from linc_convert.utils.zarr import make_compressor
+from linc_convert.utils.zarr.compressor import make_compressor
+from linc_convert.utils.zarr.zarr_config import ZarrConfig
 
 HOME = "/space/aspasia/2/users/linc/000003"
 
@@ -38,13 +39,9 @@
 @ms.default
 def convert(
     inp: list[str],
-    out: str | None = None,
     *,
-    chunk: int = 1024,
-    compressor: str = "blosc",
-    compressor_opt: str = "{}",
+    zarr_config: ZarrConfig,
     max_load: int = 16384,
-    nii: bool = False,
     orientation: str = "coronal",
     center: bool = True,
     thickness: float | None = None,
@@ -84,18 +81,8 @@ def convert(
     ----------
     inp
         Path to the input slices
-    out
-        Path to the output Zarr directory [<dirname(INP)>.ome.zarr]
-    chunk
-        Output chunk size
-    compressor : {blosc, zlib, raw}
-        Compression method
-    compressor_opt
-        Compression options
     max_load
         Maximum input chunk size
-    nii
-        Convert to nifti-zarr. True if path ends in ".nii.zarr"
     orientation
         Orientation of the slice
     center
@@ -103,6 +90,12 @@ def convert(
     thickness
         Slice thickness
     """
+    out: str = zarr_config.out
+    chunk: int = zarr_config.chunk[0]
+    compressor: str = zarr_config.compressor
+    compressor_opt: str = zarr_config.compressor_opt
+    nii: bool = zarr_config.nii
+
     # Default output path
     if not out:
         out = os.path.splitext(inp[0])[0]
diff --git a/linc_convert/modalities/df/single_slice.py b/linc_convert/modalities/df/single_slice.py
index 7bc7782d..e48a725c 100644
--- a/linc_convert/modalities/df/single_slice.py
+++ b/linc_convert/modalities/df/single_slice.py
@@ -21,7 +21,8 @@
 from linc_convert.utils.j2k import WrappedJ2K, get_pixelsize
 from linc_convert.utils.math import ceildiv
 from linc_convert.utils.orientation import center_affine, orientation_to_affine
-from linc_convert.utils.zarr import make_compressor
+from linc_convert.utils.zarr.compressor import make_compressor
+from linc_convert.utils.zarr.zarr_config import ZarrConfig
 
 ss = App(name="singleslice", help_format="markdown")
 df.command(ss)
@@ -30,13 +31,9 @@
 @ss.default
 def convert(
     inp: str,
-    out: str | None = None,
     *,
-    chunk: int = 1024,
-    compressor: str = "blosc",
-    compressor_opt: str = "{}",
+    zarr_config: ZarrConfig,
     max_load: int = 16384,
-    nii: bool = False,
     orientation: str = "coronal",
     center: bool = True,
     thickness: float | None = None,
@@ -71,18 +68,8 @@ def convert(
     ----------
     inp
         Path to the input JP2 file
-    out
-        Path to the output Zarr directory [<INP>.ome.zarr]
-    chunk
-        Output chunk size
-    compressor : {blosc, zlib, raw}
-        Compression method
-    compressor_opt
-        Compression options
     max_load
         Maximum input chunk size
-    nii
-        Convert to nifti-zarr. True if path ends in ".nii.zarr"
     orientation
         Orientation of the slice
     center
@@ -90,6 +77,12 @@ def convert(
     thickness
         Slice thickness
     """
+    out: str = zarr_config.out
+    chunk: int = zarr_config.chunk
+    compressor: str = zarr_config.compressor
+    compressor_opt: str = zarr_config.compressor_opt
+    nii: bool = zarr_config.nii
+
     if not out:
         out = os.path.splitext(inp)[0]
         out += ".nii.zarr" if nii else ".ome.zarr"
diff --git a/linc_convert/modalities/lsm/mosaic.py b/linc_convert/modalities/lsm/mosaic.py
index e02c0dba..d58b20cc 100644
--- a/linc_convert/modalities/lsm/mosaic.py
+++ b/linc_convert/modalities/lsm/mosaic.py
@@ -22,7 +22,8 @@
 from linc_convert.modalities.lsm.cli import lsm
 from linc_convert.utils.math import ceildiv
 from linc_convert.utils.orientation import center_affine, orientation_to_affine
-from linc_convert.utils.zarr import make_compressor
+from linc_convert.utils.zarr.compressor import make_compressor
+from linc_convert.utils.zarr.zarr_config import ZarrConfig
 
 mosaic = cyclopts.App(name="mosaic", help_format="markdown")
 lsm.command(mosaic)
@@ -31,13 +32,9 @@
 @mosaic.default
 def convert(
     inp: str,
-    out: str = None,
     *,
-    chunk: int = 128,
-    compressor: str = "blosc",
-    compressor_opt: str = "{}",
+    zarr_config: ZarrConfig,
     max_load: int = 512,
-    nii: bool = False,
     orientation: str = "coronal",
     center: bool = True,
     thickness: float | None = None,
@@ -72,18 +69,8 @@ def convert(
         Path to the root directory, which contains a collection of
         subfolders named `*_z{:02d}_y{:02d}*`, each containing a
         collection of files named `*_plane{:03d}_c{:d}.tiff`.
-    out
-        Path to the output Zarr directory [<INP>.ome.zarr]
-    chunk
-        Output chunk size
-    compressor : {blosc, zlib, raw}
-        Compression method
-    compressor_opt
-        Compression options
     max_load
         Maximum input chunk size when building pyramid
-    nii
-        Convert to nifti-zarr. True if path ends in ".nii.zarr".
     orientation
         Orientation of the slice
     center
@@ -91,6 +78,12 @@ def convert(
     voxel_size
         Voxel size along the X, Y and Z dimension, in micron.
     """
+    out: str = zarr_config.out
+    chunk: int = zarr_config.chunk[0]
+    compressor: str = zarr_config.compressor
+    compressor_opt: str = zarr_config.compressor_opt
+    nii: bool = zarr_config.nii
+
     if isinstance(compressor_opt, str):
         compressor_opt = ast.literal_eval(compressor_opt)
 
diff --git a/linc_convert/modalities/psoct/multi_slice.py b/linc_convert/modalities/psoct/multi_slice.py
index ca787cd1..08911e92 100644
--- a/linc_convert/modalities/psoct/multi_slice.py
+++ b/linc_convert/modalities/psoct/multi_slice.py
@@ -30,7 +30,8 @@
 from linc_convert.utils.math import ceildiv
 from linc_convert.utils.orientation import center_affine, orientation_to_affine
 from linc_convert.utils.unit import to_nifti_unit, to_ome_unit
-from linc_convert.utils.zarr import make_compressor
+from linc_convert.utils.zarr.compressor import make_compressor
+from linc_convert.utils.zarr.zarr_config import ZarrConfig, _ZarrConfig
 
 multi_slice = cyclopts.App(name="multi_slice", help_format="markdown")
 psoct.command(multi_slice)
@@ -40,13 +41,12 @@ def _automap(func: Callable) -> Callable:
     """Automatically maps the array in the mat file."""
 
     @wraps(func)
-    def wrapper(inp: list[str], out: str = None, **kwargs: dict) -> callable:
-        if out is None:
-            out = os.path.splitext(inp[0])[0]
-            out += ".nii.zarr" if kwargs.get("nii", False) else ".ome.zarr"
-        kwargs["nii"] = kwargs.get("nii", False) or out.endswith(".nii.zarr")
+    def wrapper(inp: list[str], zarr_config: _ZarrConfig, **kwargs: dict) -> callable:
+        if zarr_config.out is None:
+            zarr_config.out = os.path.splitext(inp[0])[0]
+            zarr_config.out += ".nii.zarr" if zarr_config.nii else ".ome.zarr"
         dat = _mapmat(inp, kwargs.get("key", None))
-        return func(dat, out, **kwargs)
+        return func(dat, zarr_config=zarr_config, **kwargs)
 
     return wrapper
 
@@ -163,17 +163,13 @@ def make_wrapper(fname: str) -> callable:
 @_automap
 def convert(
     inp: list[str],
-    out: Optional[str] = None,
     *,
+    zarr_config: ZarrConfig,
     key: Optional[str] = None,
     meta: str = None,
-    chunk: int = 128,
-    compressor: str = "blosc",
-    compressor_opt: str = "{}",
     max_load: int = 128,
     max_levels: int = 5,
     no_pool: Optional[int] = None,
-    nii: bool = False,
     orientation: str = "RAS",
     center: bool = True,
     dtype: str | None = None,
@@ -192,26 +188,16 @@ def convert(
     ----------
     inp
         Path to the input mat file
-    out
-        Path to the output Zarr directory [<INP>.ome.zarr]
     key
         Key of the array to be extracted, default to first key found
     meta
         Path to the metadata file
-    chunk
-        Output chunk size
-    compressor : {blosc, zlib, raw}
-        Compression method
-    compressor_opt
-        Compression options
     max_load
         Maximum input chunk size
     max_levels
         Maximum number of pyramid levels
     no_pool
         Index of dimension to not pool when building pyramid.
-    nii
-        Convert to nifti-zarr. True if path ends in ".nii.zarr"
     orientation
         Orientation of the volume
     center
@@ -219,6 +205,12 @@ def convert(
     dtype
         Data type to write into
     """
+    out: str = zarr_config.out
+    chunk: int = zarr_config.chunk[0]
+    compressor: str = zarr_config.compressor
+    compressor_opt: str = zarr_config.compressor_opt
+    nii: bool = zarr_config.nii
+
     if isinstance(compressor_opt, str):
         compressor_opt = ast.literal_eval(compressor_opt)
 
diff --git a/linc_convert/modalities/psoct/single_volume.py b/linc_convert/modalities/psoct/single_volume.py
index 529f32b4..4b2770f3 100644
--- a/linc_convert/modalities/psoct/single_volume.py
+++ b/linc_convert/modalities/psoct/single_volume.py
@@ -31,7 +31,8 @@
 from linc_convert.utils.math import ceildiv
 from linc_convert.utils.orientation import center_affine, orientation_to_affine
 from linc_convert.utils.unit import to_nifti_unit, to_ome_unit
-from linc_convert.utils.zarr import make_compressor
+from linc_convert.utils.zarr.compressor import make_compressor
+from linc_convert.utils.zarr.zarr_config import ZarrConfig, _ZarrConfig
 
 single_volume = cyclopts.App(name="single_volume", help_format="markdown")
 psoct.command(single_volume)
@@ -41,13 +42,13 @@ def _automap(func: Callable) -> Callable:
     """Automatically map the array in the mat file."""
 
     @wraps(func)
-    def wrapper(inp: str, out: str = None, **kwargs: dict) -> None:
-        if out is None:
-            out = os.path.splitext(inp[0])[0]
-            out += ".nii.zarr" if kwargs.get("nii", False) else ".ome.zarr"
-        kwargs["nii"] = kwargs.get("nii", False) or out.endswith(".nii.zarr")
+    def wrapper(inp: str, zarr_config: _ZarrConfig, **kwargs: dict) -> None:
+        if zarr_config.out is None:
+            zarr_config.out = os.path.splitext(inp[0])[0]
+            zarr_config.out += ".nii.zarr" if zarr_config.nii else ".ome.zarr"
+        # kwargs["nii"] = kwargs.get("nii", False) or out.endswith(".nii.zarr")
         with _mapmat(inp, kwargs.get("key", None)) as dat:
-            return func(dat, out, **kwargs)
+            return func(dat, zarr_config=zarr_config, **kwargs)
 
     return wrapper
 
@@ -86,17 +87,13 @@ def _mapmat(fname: str, key: str = None) -> None:
 @_automap
 def convert(
     inp: str,
-    out: Optional[str] = None,
     *,
+    zarr_config: ZarrConfig,
     key: Optional[str] = None,
     meta: str = None,
-    chunk: int = 128,
-    compressor: str = "blosc",
-    compressor_opt: str = "{}",
     max_load: int = 128,
     max_levels: int = 5,
     no_pool: Optional[int] = None,
-    nii: bool = False,
     orientation: str = "RAS",
     center: bool = True,
 ) -> None:
@@ -135,6 +132,12 @@ def convert(
     center
         Set RAS[0, 0, 0] at FOV center
     """
+    out: str = zarr_config.out
+    chunk: int = zarr_config.chunk
+    compressor: str = zarr_config.compressor
+    compressor_opt: str = zarr_config.compressor_opt
+    nii: bool = zarr_config.nii
+
     if isinstance(compressor_opt, str):
         compressor_opt = ast.literal_eval(compressor_opt)
 
diff --git a/linc_convert/modalities/wk/webknossos_annotation.py b/linc_convert/modalities/wk/webknossos_annotation.py
index 33f7b0dd..ba4b6581 100644
--- a/linc_convert/modalities/wk/webknossos_annotation.py
+++ b/linc_convert/modalities/wk/webknossos_annotation.py
@@ -16,7 +16,7 @@
 # internals
 from linc_convert.modalities.wk.cli import wk
 from linc_convert.utils.math import ceildiv
-from linc_convert.utils.zarr import make_compressor
+from linc_convert.utils.zarr.compressor import make_compressor
 
 webknossos = cyclopts.App(name="webknossos", help_format="markdown")
 wk.command(webknossos)
diff --git a/linc_convert/utils/zarr/__init__.py b/linc_convert/utils/zarr/__init__.py
new file mode 100644
index 00000000..f1882e95
--- /dev/null
+++ b/linc_convert/utils/zarr/__init__.py
@@ -0,0 +1 @@
+"""Zarr utilities."""
diff --git a/linc_convert/utils/zarr.py b/linc_convert/utils/zarr/compressor.py
similarity index 93%
rename from linc_convert/utils/zarr.py
rename to linc_convert/utils/zarr/compressor.py
index a2c031cb..76531bcd 100644
--- a/linc_convert/utils/zarr.py
+++ b/linc_convert/utils/zarr/compressor.py
@@ -1,4 +1,4 @@
-"""Zarr utilities."""
+"""Functions for zarr compression."""
 
 import numcodecs
 import numcodecs.abc
diff --git a/linc_convert/utils/zarr/zarr_config.py b/linc_convert/utils/zarr/zarr_config.py
new file mode 100644
index 00000000..68578c87
--- /dev/null
+++ b/linc_convert/utils/zarr/zarr_config.py
@@ -0,0 +1,55 @@
+"""Configuration related to output Zarr Archive."""
+
+from dataclasses import dataclass
+from typing import Annotated, Literal, Optional
+
+from cyclopts import Parameter
+
+
+@dataclass
+class _ZarrConfig:
+    """
+    Configuration related to output Zarr Archive.
+
+    Parameters
+    ----------
+    out
+        Path to the output Zarr directory [<INP>.ome.zarr]
+    chunk
+        Output chunk size.
+        Behavior depends on the number of values provided:
+        * one:   used for all spatial dimensions
+        * three: used for spatial dimensions ([z, y, x])
+        * four:  used for channels and spatial dimensions ([c, z, y, x])
+    shard
+        Output shard size.
+        If `"auto"`, find shard size that ensures files smaller than 2TB,
+        assuming a compression ratio or 2.
+    version
+        Zarr version to use. If `shard` is used, 3 is required.
+    compressor : {blosc, zlib|gzip, raw}
+        Compression method
+    compressor_opt
+        Compression options
+    nii
+        Convert to nifti-zarr. True if path ends in ".nii.zarr".
+    driver : {"zarr-python", "tensorstore", "zarrita"}
+        library used for Zarr IO Operation
+
+    """
+
+    out: Optional[str] = None
+    chunk: tuple[int] = (128,)
+    shard: list[int | str] | None = None
+    version: Literal[2, 3] = 3
+    compressor: str = "blosc"
+    compressor_opt: str = "{}"
+    nii: bool = False
+    driver: Literal["zarr-python", "tensorstore", "zarrita"] = "zarr-python"
+
+    def __post_init__(self) -> None:
+        print(self)
+        self.nii |= self.out.endswith(".nii.zarr")
+
+
+ZarrConfig = Annotated[_ZarrConfig, Parameter(name="*")]
diff --git a/pyproject.toml b/pyproject.toml
index 977e5843..a703051c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ packages = [{include = "linc_convert"}]
 
 [tool.poetry.dependencies]
 python = "^3.10"
-cyclopts = "^2.0.0"
+cyclopts = "^3.0.0"
 numpy = "*"
 nibabel = "*"
 zarr = "^2.0.0"
diff --git a/tests/test_df.py b/tests/test_df.py
index bcac8077..692dca99 100644
--- a/tests/test_df.py
+++ b/tests/test_df.py
@@ -7,6 +7,7 @@
 from helper import _cmp_zarr_archives
 
 from linc_convert.modalities.df import multi_slice
+from linc_convert.utils.zarr.zarr_config import _ZarrConfig
 
 
 def _write_test_data(directory: str) -> None:
@@ -25,5 +26,5 @@ def test_df(tmp_path):
     output_zarr = tmp_path / "output.zarr"
     files = glob.glob(os.path.join(tmp_path, "*.jp2"))
     files.sort()
-    multi_slice.convert(files, str(output_zarr))
+    multi_slice.convert(files, zarr_config=_ZarrConfig(str(output_zarr)))
     assert _cmp_zarr_archives(str(output_zarr), "data/df.zarr.zip")
diff --git a/tests/test_lsm.py b/tests/test_lsm.py
index 601da020..7f05752b 100644
--- a/tests/test_lsm.py
+++ b/tests/test_lsm.py
@@ -5,6 +5,7 @@
 from helper import _cmp_zarr_archives
 
 from linc_convert.modalities.lsm import mosaic
+from linc_convert.utils.zarr.zarr_config import _ZarrConfig
 
 
 def _write_test_data(directory: str) -> None:
@@ -24,5 +25,5 @@ def _write_test_data(directory: str) -> None:
 def test_lsm(tmp_path):
     _write_test_data(tmp_path)
     output_zarr = tmp_path / "output.zarr"
-    mosaic.convert(str(tmp_path), str(output_zarr))
+    mosaic.convert(str(tmp_path), zarr_config=_ZarrConfig(str(output_zarr)))
     assert _cmp_zarr_archives(str(output_zarr), "data/lsm.zarr.zip")
diff --git a/tests/test_wk.py b/tests/test_wk.py
index f4c3704a..31294af2 100644
--- a/tests/test_wk.py
+++ b/tests/test_wk.py
@@ -1,4 +1,3 @@
-
 import os
 
 import numpy as np
@@ -10,95 +9,92 @@
 
 
 def _write_test_data(directory: str) -> None:
-    wkw_dir = f'{directory}/wkw'
-    ome_dir = f'{directory}/ome'
+    wkw_dir = f"{directory}/wkw"
+    ome_dir = f"{directory}/ome"
 
     store = zarr.storage.DirectoryStore(ome_dir)
     omz = zarr.group(store=store, overwrite=True)
 
     for level in range(5):
-        size = 2**(4-level)
+        size = 2 ** (4 - level)
         wkw_array = np.zeros((size, size, 5), dtype=np.uint8)
         ome_array = np.zeros((1, 5, size, size), dtype=np.uint8)
 
-        wkw_filepath = os.path.join(wkw_dir, get_mask_name(level)) 
+        wkw_filepath = os.path.join(wkw_dir, get_mask_name(level))
         with wkw.Dataset.create(wkw_filepath, wkw.Header(np.uint8)) as dataset:
             dataset.write((0, 0, 0), wkw_array)
 
-        omz.create_dataset(f'{level}', shape=[1, 5, size, size])
-        array = omz[f'{level}']
-        array[...] = ome_array 
+        omz.create_dataset(f"{level}", shape=[1, 5, size, size])
+        array = omz[f"{level}"]
+        array[...] = ome_array
 
-    multiscales = [{
-            'version': '0.4',
-            'axes': [
+    multiscales = [
+        {
+            "version": "0.4",
+            "axes": [
                 {"name": "c", "type": "space", "unit": "millimeter"},
                 {"name": "z", "type": "space", "unit": "millimeter"},
                 {"name": "y", "type": "space", "unit": "micrometer"},
-                {"name": "x", "type": "space", "unit": "micrometer"}
+                {"name": "x", "type": "space", "unit": "micrometer"},
             ],
-            'datasets': [],
-            'type': 'jpeg2000',
-            'name': '',
-        }] 
+            "datasets": [],
+            "type": "jpeg2000",
+            "name": "",
+        }
+    ]
     for n in range(5):
-        multiscales[0]['datasets'].append({})
-        level = multiscales[0]['datasets'][-1]
+        multiscales[0]["datasets"].append({})
+        level = multiscales[0]["datasets"][-1]
         level["path"] = str(n)
 
         level["coordinateTransformations"] = [
             {
                 "type": "scale",
                 "scale": [
-                    1.0, 
-                    1.0, 
+                    1.0,
+                    1.0,
                     float(2**n),
                     float(2**n),
-                ]
+                ],
             },
             {
                 "type": "translation",
                 "translation": [
-                    0.0, 
-                    0.0, 
-                    float(2**n - 1) *0.5,
-                    float(2**n - 1) *0.5,
-                ]
-            }
+                    0.0,
+                    0.0,
+                    float(2**n - 1) * 0.5,
+                    float(2**n - 1) * 0.5,
+                ],
+            },
         ]
     omz.attrs["multiscales"] = multiscales
 
 
-
-
 def test_wk(tmp_path):
     _write_test_data(tmp_path)
 
     wkw_dir = str(tmp_path / "wkw")
     ome_dir = str(tmp_path / "ome")
-    basename = os.path.basename(ome_dir)[:-9] 
-    initials = wkw_dir.split('/')[-2][:2]
-    output_zarr = os.path.join(tmp_path, basename + '_dsec_' + initials + '.ome.zarr')
+    basename = os.path.basename(ome_dir)[:-9]
+    initials = wkw_dir.split("/")[-2][:2]
+    output_zarr = os.path.join(tmp_path, basename + "_dsec_" + initials + ".ome.zarr")
 
     print("starting the convert process")
     webknossos_annotation.convert(wkw_dir, ome_dir, tmp_path, "{}")
 
-    z = zarr.open(output_zarr, mode='r')
+    z = zarr.open(output_zarr, mode="r")
     for level in range(5):
         print("output_zarr has", np.shape(z[level]), np.unique(z[level]))
 
-    z = zarr.open('data/wk.zarr.zip', mode='r')
+    z = zarr.open("data/wk.zarr.zip", mode="r")
     for level in range(5):
         print("trusted result has", np.shape(z[level]), np.unique(z[level]))
-  
 
     assert _cmp_zarr_archives(str(output_zarr), "data/wk.zarr.zip")
 
 
-
 def get_mask_name(level):
     if level == 0:
-        return '1'
+        return "1"
     else:
-        return f'{2**level}-{2**level}-1'
-
+        return f"{2**level}-{2**level}-1"