diff --git a/pyproject.toml b/pyproject.toml
index e65f787..62e12ee 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "softcopy"
-version = "0.0.2"
+version = "0.0.10"
 description = "Copies zarr archives from an acquisition frontend to a different disk, using filesystem watching and lockfiles to allow copying during acquisition."
 authors = [{ name = "Seth Hinz", email = "sethhinz@me.com" }]
 readme = "README.md"
@@ -34,6 +34,7 @@ dev-dependencies = [
     "mypy>=0.991",
     "ruff>=0.0.235",
     "pytest-cov>=5.0.0",
+    "iohub>=0.2.0",
 ]
 
 [build-system]
diff --git a/softcopy/hcs_copier.py b/softcopy/hcs_copier.py
new file mode 100644
index 0000000..bcfe641
--- /dev/null
+++ b/softcopy/hcs_copier.py
@@ -0,0 +1,142 @@
+import logging
+import shutil
+from pathlib import Path
+from threading import Event, Thread
+
+import iohub
+
+from .copier import AbstractCopier
+from .zarr_copier import ZarrCopier
+
+logging.basicConfig(level=logging.DEBUG, format="[%(asctime)s : %(levelname)s from %(name)s] %(message)s")
+LOG = logging.getLogger(__name__)
+
+
+def get_all_zarr_paths(plate_path: Path) -> list[Path]:
+    plate: iohub.ngff.Plate = iohub.open_ome_zarr(plate_path)
+    wells = plate.wells()
+    zarr_paths = []
+
+    for _, well in wells:
+        for _, pos in well.positions():
+            for _, image in pos.images():
+                zarr_paths.append(Path(image._attrs.store.path) / Path(image._attrs.key).parent)
+
+    return zarr_paths
+
+
+def create_metadata_path_mapping(source: Path, destination: Path) -> list[tuple[Path, Path]]:
+    path_mappings = []
+    plate: iohub.ngff.Plate = iohub.open_ome_zarr(source)
+
+    for metadata_file in [".zattrs", ".zgroup"]:
+        src_metadata_path = source / metadata_file
+        dest_metadata_path = destination / metadata_file
+        path_mappings.append((src_metadata_path, dest_metadata_path))
+
+    for row, _ in plate.rows():
+        src = source / row
+        dest = destination / row
+        for metadata_file in [".zattrs", ".zgroup"]:
+            src_metadata_path = src / metadata_file
+            dest_metadata_path = dest / metadata_file
+            path_mappings.append((src_metadata_path, dest_metadata_path))
+
+    for well_path_component, well in plate.wells():
+        well_src = source / well_path_component
+        well_dest = destination / well_path_component
+        for metadata_file in [".zattrs", ".zgroup"]:
+            src_metadata_path = well_src / metadata_file
+            dest_metadata_path = well_dest / metadata_file
+            path_mappings.append((src_metadata_path, dest_metadata_path))
+
+        for pos_path_component, _ in well.positions():
+            src = well_src / pos_path_component
+            dest = well_dest / pos_path_component
+            for metadata_file in [".zattrs", ".zgroup"]:
+                src_metadata_path = src / metadata_file
+                dest_metadata_path = dest / metadata_file
+                path_mappings.append((src_metadata_path, dest_metadata_path))
+
+    return path_mappings
+
+
+class SlowCopier(Thread):
+    def __init__(self, path_mappings: list[tuple[Path, Path]]):
+        super().__init__()
+        self.path_mappings = path_mappings
+        self.stop_event = Event()
+        self.last_copy_times = {dest: None for _, dest in path_mappings}
+
+    def _copy_pass(self):
+        for source, destination in self.path_mappings:
+            try:
+                if source.exists():
+                    source_mtime = source.stat().st_mtime
+                    last_copy_time = self.last_copy_times[destination]
+
+                    if last_copy_time is None or source_mtime > last_copy_time:
+                        shutil.copy2(source, destination)
+                        self.last_copy_times[destination] = source.stat().st_mtime
+                        LOG.debug(f"Copied {source} to {destination}")
+                else:
+                    LOG.debug(f"Source file {source} does not exist yet.")
+            except Exception as e:
+                LOG.exception(f"Error copying {source} to {destination}: {e}")  # noqa: TRY401
+
+    def run(self):
+        while not self.stop_event.is_set():
+            self._copy_pass()
+            self.stop_event.wait(0.1)  # Sleep for 0.1 seconds or until stop_event is set
+
+    def join(self):
+        self.stop_event.set()
+        super().join()  # Wait for the thread to finish
+        self._copy_pass()  # Final copy pass to ensure all files are copied
+
+
+class HCSCopier(AbstractCopier):
+    _copiers: list[ZarrCopier]
+    _metadata_copier: SlowCopier
+
+    def __init__(
+        self,
+        source: Path,
+        destination: Path,
+        n_copy_procs: int,
+        sleep_time: float = 0,
+        wait_for_source: bool = True,
+        log: logging.Logger = LOG,
+    ):
+        super().__init__(source, destination, n_copy_procs, sleep_time, log)
+
+        image_paths = get_all_zarr_paths(source)
+        print(image_paths)
+        self._copiers = []
+        for image_path in image_paths:
+            image_destination = destination / image_path.relative_to(source)
+            print(image_destination)
+            image_destination.mkdir(parents=True, exist_ok=True)
+            zarr_copier = ZarrCopier(image_path, image_destination, n_copy_procs, sleep_time, wait_for_source, log)
+            self._copiers.append(zarr_copier)
+
+        path_map = create_metadata_path_mapping(source, destination)
+        self._metadata_copier = SlowCopier(path_map)
+
+    def start(self):
+        # Before starting, we make the parent directory that the image will be copied into.
+        self._destination.mkdir(parents=True, exist_ok=True)
+        for copier in self._copiers:
+            copier.start()
+        self._metadata_copier.start()
+
+    def join(self):
+        for copier in self._copiers:
+            copier.join()
+        self._metadata_copier.join()
+
+    def stop(self):
+        for copier in self._copiers:
+            copier.stop()
+
+        self._metadata_copier.join()
diff --git a/softcopy/main.py b/softcopy/main.py
index 1a895b6..cb4d0f3 100644
--- a/softcopy/main.py
+++ b/softcopy/main.py
@@ -4,11 +4,9 @@
 
 import click
 import psutil
-import yaml
 from psutil import AccessDenied
 
-from .copier import AbstractCopier
-from .ome_zarr_copier import OMEZarrCopier
+from .hcs_copier import HCSCopier
 from .zarr_copier import ZarrCopier
 
 BOLD_SEQ = "\033[1m"
@@ -17,7 +15,8 @@
 
 
 @click.command()
-@click.argument("targets_file", type=click.File("r"))
+@click.argument("source-path", type=click.Path(file_okay=False, dir_okay=True, path_type=Path))
+@click.argument("dest-path", type=click.Path(file_okay=False, dir_okay=True, path_type=Path))
 @click.option("--verbose", default=False, is_flag=True, help="print debug information while running")
 @click.option("--nprocs", default=1, type=int, help="number of processes to use for copying")
 @click.option(
@@ -31,7 +30,7 @@
     default=True,
     help="If the source does not exist when softcopy is started, wait for it to appear. If false, softcopy will crash if the source does not exist",
 )
-def main(targets_file, verbose, nprocs, sleep_time, wait_for_source):
+def main(source_path, dest_path, verbose, nprocs, sleep_time, wait_for_source):
     """Tranfer data from source to destination as described in a yaml TARGETS_FILE. Uses low priority io to allow
     data to be moved while the microscope is acquiring. The program is zarr-aware and can safely copy an archive
     before it is finished being written to."""
@@ -40,40 +39,49 @@ def main(targets_file, verbose, nprocs, sleep_time, wait_for_source):
     LOG.setLevel(log_level)
     logging.basicConfig(format="[%(asctime)s : %(levelname)s from %(name)s] " + BOLD_SEQ + "%(message)s" + RESET_SEQ)
 
-    # Load the yaml at a normal io priority because it is small and likely not on
-    # the target disk
-    all_yaml = yaml.safe_load(targets_file)
-    targets = all_yaml["targets"]
-    LOG.debug(f"Number of targets: {len(targets)}")
-
-    # Now that we have the yaml, we floor our io priority. We are about to read zarr metadata, and even doing that
-    # at the wrong time could slow down the writer process!
     set_low_io_priority()
 
-    copiers: list[AbstractCopier] = []
-
-    # TODO: actually run the copiers in parallel
+    try:
+        source_path = source_path.expanduser().absolute()
+        dest_path = dest_path.expanduser().absolute()
+    except Exception:
+        LOG.exception("Error expanding paths")
+        sys.exit(1)
+
+    filetype_map = {
+        ".ome.zarr": HCSCopier,
+        ".zarr": ZarrCopier,
+    }
+
+    source_type = source_path.suffix.lower()
+    if source_type not in filetype_map:
+        LOG.error(
+            f"Unsupported source file type: {source_path.suffix}. Supported types are: {list(filetype_map.keys())}"
+        )
+        sys.exit(1)
+
+    copier_class = filetype_map[source_type]
+    copier = copier_class(
+        source_path,
+        dest_path,
+        n_copy_procs=nprocs,
+        sleep_time=sleep_time,
+        wait_for_source=wait_for_source,
+        log=LOG.getChild("Copier"),
+    )
 
     try:
-        for target_id, target in enumerate(targets):
-            source = Path(target["source"]).expanduser().absolute()
-            destination = Path(target["destination"]).expanduser().absolute()
-            # If the source ends with .ome.zarr, then infer ome mode for this entry:
-            is_ome = source.name.endswith(".ome.zarr")
-            copier_type = OMEZarrCopier if is_ome else ZarrCopier
-            copier = copier_type(
-                source, destination, nprocs, sleep_time, wait_for_source, LOG.getChild(f"Target {target_id}")
-            )
-            copiers.append(copier)
-            copier.start()
-
-        # Wait for all copiers to finish
-        for copier in copiers:
-            copier.join()
+        LOG.info(f"Starting copy from {source_path} to {dest_path} using {copier_class.__name__}")
+        copier.start()
+        copier.join()
+        LOG.info("Copy completed successfully.")
     except KeyboardInterrupt:
-        LOG.info("Keyboard interrupt recieved, stopping all copiers")
-        for copier in copiers:
-            copier.stop()
+        LOG.info("Keyboard interrupt received, stopping copier.")
+        copier.stop()
+    except Exception:
+        LOG.exception("An error occurred during copying")
+        copier.stop()
+        sys.exit(1)
 
 
 def set_low_io_priority():
diff --git a/softcopy/ome_zarr_copier.py b/softcopy/ome_zarr_copier.py
deleted file mode 100644
index 718e0ab..0000000
--- a/softcopy/ome_zarr_copier.py
+++ /dev/null
@@ -1,80 +0,0 @@
-import hashlib
-import logging
-import shutil
-from pathlib import Path
-from typing import ClassVar
-
-from .copier import AbstractCopier
-from .zarr_copier import ZarrCopier
-
-LOG = logging.getLogger(__name__)
-
-
-class OMEZarrCopier(AbstractCopier):
-    """
-    Wrapper around a ZarrCopier that also copies the metadata files for an OME-Zarr archive.
-    """
-
-    # Files in the ome zarr archive that, if present, should be copied to the destination.
-    # Importantly, note that these files are all small - we assume they can be loaded into memory.
-    METADATA_FILES: ClassVar[list] = [
-        ".zattrs",
-        ".zgroup",
-        ".zarray",
-        "zarr.json",
-        "daxi.json",
-    ]
-
-    _zarr_copier: ZarrCopier
-    _metadata_hashes: dict[str, str]
-
-    def __init__(
-        self,
-        source: Path,
-        destination: Path,
-        n_copy_procs: int,
-        sleep_time: float = 0,
-        wait_for_source: bool = True,
-        log: logging.Logger = LOG,
-    ):
-        super().__init__(source, destination, n_copy_procs, sleep_time, log)
-        image_0_source = source / "0"
-        image_0_destination = destination / "0"
-        self._zarr_copier = ZarrCopier(
-            image_0_source, image_0_destination, n_copy_procs, sleep_time, wait_for_source, log
-        )
-        self._metadata_hashes = {}
-
-    def start(self):
-        # Before starting, we make the parent directory that the image will be copied into.
-        self._destination.mkdir(parents=True, exist_ok=True)
-        self._zarr_copier.start()
-
-    def join(self):
-        self._zarr_copier.join()
-        self.copy_metadata_files()
-
-    def stop(self):
-        self._zarr_copier.stop()
-        self.copy_metadata_files()
-
-    def copy_metadata_files(self):
-        for metadata_file in self.METADATA_FILES:
-            source_file = self._source / metadata_file
-            destination_file = self._destination / metadata_file
-            if source_file.exists():
-                file_hash = hashlib.md5(source_file.read_bytes()).hexdigest()  # noqa: S324 (this hash is not cryptographically relevant)
-
-                if metadata_file in self._metadata_hashes and self._metadata_hashes[metadata_file] == file_hash:
-                    self._log.debug(f"Metadata file {source_file} (hash {file_hash}) is unchanged, skipping")
-                    continue
-
-                self._log.debug(f"Copying metadata file {source_file} (hash {file_hash}) to {destination_file}")
-
-                # The line below is not needed in this specific use case but it's forseeable that the directory might
-                # not exist for certain files... leaving this out for now.
-                # destination_file.parent.mkdir(parents=True, exist_ok=True)
-
-                shutil.copy2(source_file, destination_file)
-            else:
-                self._log.debug(f"Metadata file {source_file} does not exist, skipping")
diff --git a/softcopy/zarr_copier.py b/softcopy/zarr_copier.py
index a35cd9f..49b3aa3 100644
--- a/softcopy/zarr_copier.py
+++ b/softcopy/zarr_copier.py
@@ -180,7 +180,7 @@ def stop(self):
             self._observer.stop()
             self._observer.join()
 
-    def join(self):
+    def join(self):  # noqa: C901
         time_start = time.time()
         estimated_files = np.prod(self._files_nd)
 
@@ -220,7 +220,7 @@ def print_copy_status():
             # This is a very long io-bound method - so we need to be able to exit it with ctrl c
             if self._stop.value == 1:
                 return
-            
+
             chunk_packed_name: PackedName = PackedName.from_index(chunk_index)
             chunk_path = chunk_packed_name.get_path(
                 self._files_nd, self._destination, self._dimension_separator, self._zarr_format
diff --git a/tests/test_hcs_copier.py b/tests/test_hcs_copier.py
new file mode 100644
index 0000000..e68b23c
--- /dev/null
+++ b/tests/test_hcs_copier.py
@@ -0,0 +1,126 @@
+import multiprocessing as mp
+import random
+import subprocess
+import tempfile
+import time
+from pathlib import Path
+from threading import Event, Thread
+
+import iohub
+import iohub.ngff
+import numpy as np
+import pytest
+import tensorstore as ts
+from test_softcopy import run_softcopy
+
+
+def slow_write(target: Path):
+    shape = [5, 4, 100, 100, 100]
+    z_chunk = 20
+    archive = ts.open({
+        "driver": "zarr",
+        "kvstore": {
+            "driver": "file",
+            "path": str(target),
+        },
+        "metadata": {
+            "compressor": {
+                "id": "blosc",
+                "cname": "blosclz",
+                "shuffle": 1,
+                "clevel": 3,
+            },
+            "dtype": "<u2",
+            "shape": shape,
+            "chunks": [1, 1, z_chunk, 30, 40],
+            "dimension_separator": "/",
+        },
+        "create": True,
+        "delete_existing": True,
+    }).result()
+
+    time.sleep(random.uniform(1, 2))  # noqa: S311
+
+    random_slab = np.random.randint(0, 65536, size=(z_chunk, *shape[-2:]), dtype="<u2")
+    for t in range(shape[0]):
+        for v in range(shape[1]):
+            for z_index in range(0, shape[2], z_chunk):
+                archive[t, v, z_index : z_index + z_chunk, ...].write(random_slab).result()
+                time.sleep(random.uniform(0.1, 0.5))  # noqa: S311
+
+
+def slow_write_hcs(target: Path, start_barrier: Event):
+    plate = iohub.open_ome_zarr(
+        target,
+        "hcs",
+        "w",
+        channel_names=["a", "b"],
+    )
+
+    start_barrier.wait()
+
+    targets: list[Path] = []
+    for camera in ("cam1", "cam2"):
+        for color in ("488nm", "561nm", "640nm"):
+            for pos in ("pos1", "pos2", "pos3"):
+                pos: iohub.ngff.Position = plate.create_position(camera, color, pos)
+
+                for image, scale in enumerate([[1] * 5, [1, 1, 0.25, 0.25, 0.25]]):
+                    pos._create_image_meta(str(image), [iohub.ngff.TransformationMeta(type="scale", scale=scale)])
+
+                    targets.append(Path(pos.zattrs.store.path) / Path(pos.zattrs.key).parent / str(image))
+    plate.wells()
+
+    threads = []
+    for target in targets:
+        thread = Thread(target=slow_write, args=(target,))
+        thread.start()
+        threads.append(thread)
+
+    for thread in threads:
+        thread.join()
+
+
+def test_hcs_copier():
+    root_path = Path(tempfile.mkdtemp())
+    plate_path = root_path / "plate.ome.zarr"
+    print(plate_path)
+    start_barrier = Event()
+    thread = Thread(target=slow_write_hcs, args=(plate_path, start_barrier))
+    thread.start()
+    start_barrier.set()
+    time.sleep(5)
+
+    ctx = mp.get_context("spawn")
+    softcopy_process = ctx.Process(target=run_softcopy, args=(plate_path, root_path / "copy.ome.zarr"))
+    softcopy_process.start()
+
+    # from softcopy.hcs_copier import HCSCopier
+
+    # copier = HCSCopier(plate_path, root_path / "copy.ome.zarr", 4)
+
+    # copier.start()
+
+    thread.join()
+
+    softcopy_process.join(timeout=120)
+
+    if softcopy_process.is_alive():
+        softcopy_process.terminate()
+        pytest.fail("softcopy process did not complete in 2 minutes")
+
+    # copier.stop()
+    # copier.join()
+
+    def compare_directories(dir1: Path, dir2: Path):
+        result = subprocess.run(  # noqa: S602
+            f"diff -qr {dir1} {dir2} | grep -E 'Only in|Files .* differ'", shell=True, capture_output=True, text=True
+        )
+        return result.stdout.strip()
+
+    # compare_directories(plate_path, root_path / "copy.ome.zarr")
+    assert not compare_directories(plate_path, root_path / "copy.ome.zarr"), "Directories differ after copying"
+
+
+if __name__ == "__main__":
+    test_hcs_copier()
diff --git a/tests/test_softcopy.py b/tests/test_softcopy.py
index e5ff517..1418c9e 100644
--- a/tests/test_softcopy.py
+++ b/tests/test_softcopy.py
@@ -1,12 +1,10 @@
 import multiprocessing as mp
-import shutil
 import time
 from pathlib import Path
 
 import numpy as np
 import pytest
 import tensorstore as ts
-import yaml
 
 import softcopy
 import softcopy.main
@@ -20,28 +18,16 @@ def run_slow_write(dummy_path: Path, input_path: Path, no_complete_file: bool =
     )
 
 
-def run_softcopy(targets_file_path: Path):
+def run_softcopy(source_path: Path, dest_path: Path):
     softcopy.main.main(
         [
-            str(targets_file_path),
+            str(source_path),
+            str(dest_path),
         ],
         standalone_mode=False,
     )
 
 
-def create_targets_yaml(targets_file_path: Path, input_path: Path, output_path: Path):
-    targets = {
-        "targets": [
-            {
-                "source": str(input_path),
-                "destination": str(output_path),
-            }
-        ]
-    }
-    with open(targets_file_path, "w") as f:
-        f.write(yaml.dump(targets))
-
-
 def wait_for_file(file_path: Path, timeout: int = 120):
     start_time = time.time()
     while not file_path.exists():
@@ -51,15 +37,11 @@ def wait_for_file(file_path: Path, timeout: int = 120):
 
 
 def test_slow_write_and_softcopy(workspace, dummy_zarr_path, create_zarr2_archive):
-    input_path = workspace / "input"
-    output_path = workspace / "output"
-    targets_file_path = workspace / "targets.yaml"
-
-    create_targets_yaml(targets_file_path, input_path, output_path)
+    input_path = workspace / "input.zarr"
+    output_path = workspace / "output.zarr"
 
     ctx = mp.get_context("spawn")
     slow_write_process = ctx.Process(target=run_slow_write, args=(dummy_zarr_path, input_path))
-    # use spawn instead:
     slow_write_process.start()
 
     try:
@@ -68,7 +50,7 @@ def test_slow_write_and_softcopy(workspace, dummy_zarr_path, create_zarr2_archiv
         slow_write_process.terminate()
         pytest.fail("slow_write process did not start in time")
 
-    softcopy_process = ctx.Process(target=run_softcopy, args=(targets_file_path,))
+    softcopy_process = ctx.Process(target=run_softcopy, args=(input_path, output_path))
     softcopy_process.start()
 
     slow_write_process.join(timeout=120)
@@ -96,82 +78,82 @@ def test_slow_write_and_softcopy(workspace, dummy_zarr_path, create_zarr2_archiv
     assert np.all(np.equal(slow_write_output[:].read().result(), copied_dataset[:].read().result()))
 
 
-# In the tests above, we just test copying a regular zarr archive. However, we also need limited support for ome-zarr FOV data.
-# Specifically, the ome-zarr subset that is written by DaXi. This looks like the following:
-# aquisition.ome.zarr/
-# - .zgroup # .zgroup and .zattrs are modified only at the acquisition start
-# - .zattrs
-# - daxi.json # daxi.json is appended to at each timepoint
-# - daxi.json.temp # Sometimes exists, doesn't need to be copied
-# - 0/ # this is a normal, /-delimited zarr 2 archive.
-#   - .zarray
-#   - 0/
-#     - 0/
-#     - ...
-# This test is thus almost the same as the previous one, but with a more complicated skeleton. Additionally, as slow_write can only
-# output zarr (not ome zarr), we just use slow write to output to the 0/ folder, and then invoke softcopy on the entire .ome.zarr
-# folder.
-def test_slow_write_and_softcopy_ome_zarr(workspace, dummy_zarr_path, create_zarr2_archive):
-    # Construct a dummy acquisition
-    input_path = workspace / "input.ome.zarr"
-    input_path.mkdir()
-    (input_path / ".zgroup").write_text(".zgroup")
-    (input_path / ".zattrs").write_text(".zattrs")
-
-    output_path = workspace / "output.ome.zarr"
-    targets_file_path = workspace / "targets.yaml"
-
-    create_targets_yaml(targets_file_path, input_path, output_path)
-
-    ctx = mp.get_context("spawn")
-    slow_write_process = ctx.Process(target=run_slow_write, args=(dummy_zarr_path, input_path / "0", True))
-    slow_write_process.start()
-
-    try:
-        wait_for_file(input_path / "0" / ".zarray")
-    except TimeoutError:
-        slow_write_process.terminate()
-        pytest.fail("slow_write process did not start in time")
-
-    # Start softcopy and disable the complete file so that we can tamper with daxi.json
-    # before the write is complete
-    softcopy_process = ctx.Process(target=run_softcopy, args=(targets_file_path,))
-    softcopy_process.start()
-
-    # Wait for all of the data to be done writing
-    slow_write_process.join(timeout=120)
-    if slow_write_process.is_alive():
-        slow_write_process.terminate()
-        pytest.fail("slow_write process did not complete in 2 minutes")
-
-    # Modify daxi.json via daxi.json.temp and shutil.move
-    daxi_json_temp = input_path / "daxi.json.temp"
-    daxi_json = input_path / "daxi.json"
-    daxi_json_temp.write_text("daxi.json")
-    shutil.move(daxi_json_temp, daxi_json)
-
-    # Create the complete file to signal that the write is done
-    (input_path / "0" / "complete").touch()
-
-    softcopy_process.join(timeout=120)
-
-    if softcopy_process.is_alive():
-        softcopy_process.terminate()
-        pytest.fail("softcopy process did not complete in 2 minutes")
-
-    slow_write_output = ts.open({
-        "driver": "zarr",
-        "kvstore": {"driver": "file", "path": str(input_path / "0")},
-    }).result()
-
-    assert (output_path / ".zgroup").exists() and (output_path / ".zgroup").read_text() == ".zgroup"
-    assert (output_path / ".zattrs").exists() and (output_path / ".zattrs").read_text() == ".zattrs"
-    assert (output_path / "daxi.json").exists() and (output_path / "daxi.json").read_text() == "daxi.json"
-    assert not (output_path / "daxi.json.temp").exists()
-
-    copied_dataset = ts.open({
-        "driver": "zarr",
-        "kvstore": {"driver": "file", "path": str(output_path / "0")},
-    }).result()
-
-    assert np.all(np.equal(slow_write_output[:].read().result(), copied_dataset[:].read().result()))
+# # In the tests above, we just test copying a regular zarr archive. However, we also need limited support for ome-zarr FOV data.
+# # Specifically, the ome-zarr subset that is written by DaXi. This looks like the following:
+# # aquisition.ome.zarr/
+# # - .zgroup # .zgroup and .zattrs are modified only at the acquisition start
+# # - .zattrs
+# # - daxi.json # daxi.json is appended to at each timepoint
+# # - daxi.json.temp # Sometimes exists, doesn't need to be copied
+# # - 0/ # this is a normal, /-delimited zarr 2 archive.
+# #   - .zarray
+# #   - 0/
+# #     - 0/
+# #     - ...
+# # This test is thus almost the same as the previous one, but with a more complicated skeleton. Additionally, as slow_write can only
+# # output zarr (not ome zarr), we just use slow write to output to the 0/ folder, and then invoke softcopy on the entire .ome.zarr
+# # folder.
+# def test_slow_write_and_softcopy_ome_zarr(workspace, dummy_zarr_path, create_zarr2_archive):
+#     # Construct a dummy acquisition
+#     input_path = workspace / "input.ome.zarr"
+#     input_path.mkdir()
+#     (input_path / ".zgroup").write_text(".zgroup")
+#     (input_path / ".zattrs").write_text(".zattrs")
+
+#     output_path = workspace / "output.ome.zarr"
+#     targets_file_path = workspace / "targets.yaml"
+
+#     create_targets_yaml(targets_file_path, input_path, output_path)
+
+#     ctx = mp.get_context("spawn")
+#     slow_write_process = ctx.Process(target=run_slow_write, args=(dummy_zarr_path, input_path / "0", True))
+#     slow_write_process.start()
+
+#     try:
+#         wait_for_file(input_path / "0" / ".zarray")
+#     except TimeoutError:
+#         slow_write_process.terminate()
+#         pytest.fail("slow_write process did not start in time")
+
+#     # Start softcopy and disable the complete file so that we can tamper with daxi.json
+#     # before the write is complete
+#     softcopy_process = ctx.Process(target=run_softcopy, args=(targets_file_path,))
+#     softcopy_process.start()
+
+#     # Wait for all of the data to be done writing
+#     slow_write_process.join(timeout=120)
+#     if slow_write_process.is_alive():
+#         slow_write_process.terminate()
+#         pytest.fail("slow_write process did not complete in 2 minutes")
+
+#     # Modify daxi.json via daxi.json.temp and shutil.move
+#     daxi_json_temp = input_path / "daxi.json.temp"
+#     daxi_json = input_path / "daxi.json"
+#     daxi_json_temp.write_text("daxi.json")
+#     shutil.move(daxi_json_temp, daxi_json)
+
+#     # Create the complete file to signal that the write is done
+#     (input_path / "0" / "complete").touch()
+
+#     softcopy_process.join(timeout=120)
+
+#     if softcopy_process.is_alive():
+#         softcopy_process.terminate()
+#         pytest.fail("softcopy process did not complete in 2 minutes")
+
+#     slow_write_output = ts.open({
+#         "driver": "zarr",
+#         "kvstore": {"driver": "file", "path": str(input_path / "0")},
+#     }).result()
+
+#     assert (output_path / ".zgroup").exists() and (output_path / ".zgroup").read_text() == ".zgroup"
+#     assert (output_path / ".zattrs").exists() and (output_path / ".zattrs").read_text() == ".zattrs"
+#     assert (output_path / "daxi.json").exists() and (output_path / "daxi.json").read_text() == "daxi.json"
+#     assert not (output_path / "daxi.json.temp").exists()
+
+#     copied_dataset = ts.open({
+#         "driver": "zarr",
+#         "kvstore": {"driver": "file", "path": str(output_path / "0")},
+#     }).result()
+
+#     assert np.all(np.equal(slow_write_output[:].read().result(), copied_dataset[:].read().result()))
diff --git a/tests/test_to_ome.py b/tests/test_to_ome.py
deleted file mode 100644
index 6f26ed3..0000000
--- a/tests/test_to_ome.py
+++ /dev/null
@@ -1,25 +0,0 @@
-import numpy as np
-
-from softcopy.to_ome import main
-
-
-def test_full_run(dummy_zarr_path, create_zarr2_archive):
-    # Invoke the `main` function (i.e. the cli) to convert to ome zarr
-    main([str(dummy_zarr_path), "--run"], standalone_mode=False)
-
-    data = create_zarr2_archive["data"]
-    chunks = create_zarr2_archive["chunks"]
-    files_nd = np.floor_divide(data.shape, chunks)
-
-    # Check that the ome zarr archive was created
-    for chunk_id in np.ndindex(*files_nd):
-        assert (dummy_zarr_path / "0" / "/".join(map(str, chunk_id))).exists()
-
-    # Ensure that the contents of the ome zarr archive (non recursive) is just
-    # .zattrs, .zgroup, and the data folder, "0/":
-    top_level_contents = {node.name for node in dummy_zarr_path.iterdir()}
-    expected_contents = {".zattrs", ".zgroup", "0"}
-    assert top_level_contents == expected_contents
-
-
-# TODO: test for / dimension separator input, remove dim
diff --git a/uv.lock b/uv.lock
index f473ea3..2d42aea 100644
--- a/uv.lock
+++ b/uv.lock
@@ -6,6 +6,53 @@ resolution-markers = [
     "python_full_version >= '3.13'",
 ]
 
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+[[package]]
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+
+[[package]]
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+version = "3.4.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "msgpack" },
+    { name = "ndindex" },
+    { name = "numexpr", marker = "platform_machine != 'wasm32'" },
+    { name = "numpy" },
+    { name = "platformdirs" },
+    { name = "py-cpuinfo", marker = "platform_machine != 'wasm32'" },
+    { name = "requests" },
+]
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+    { url = "https://files.pythonhosted.org/packages/32/00/2dceb6dcc368855622739838bb16475f96590f8dc4939c1d69f23a03f652/blosc2-3.4.0-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:64170a2e7b3dc92ceb39e94f53efc3b832e8128cd885451d610872ebd7899e93", size = 3364081 },
+    { url = "https://files.pythonhosted.org/packages/76/a6/198ef6f6337cda8ed9d8dd9375dd9233aeb1a8140b1cb20f3333ce1487b5/blosc2-3.4.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:526860d068577b31c42fdd11b0c0f19625e0ff49e8829cff84275a78b9cabf78", size = 4269001 },
+    { url = "https://files.pythonhosted.org/packages/e3/23/bfbab0ea02070354a5ec4cea2695f7181f21b2516f743a7182046d8cb5e2/blosc2-3.4.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:44ccbc0066714857548e281c1376b2a2c77dba7be088e83f3d31c750da6fb97e", size = 4412607 },
+    { url = "https://files.pythonhosted.org/packages/fc/db/edd58976c587379078ae5e6ee1782175bc3abad3834cdd54ff0e14e60e81/blosc2-3.4.0-cp313-cp313-win_amd64.whl", hash = "sha256:976e8b7e1603d15f8a83c87fdbfe7c60082b878b79a6676eeefc4cbb57c3141b", size = 2193708 },
+]
+
 [[package]]
 name = "cachetools"
 version = "5.5.0"
@@ -15,6 +62,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/a4/07/14f8ad37f2d12a5ce41206c21820d8cb6561b728e51fad4530dff0552a67/cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292", size = 9524 },
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+[[package]]
+name = "certifi"
+version = "2025.6.15"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/73/f7/f14b46d4bcd21092d7d3ccef689615220d8a08fb25e564b65d20738e672e/certifi-2025.6.15.tar.gz", hash = "sha256:d747aa5a8b9bbbb1bb8c22bb13e22bd1f18e9796defa16bab421f7f7a317323b", size = 158753 }
+wheels = [
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+]
+
 [[package]]
 name = "cfgv"
 version = "3.4.0"
@@ -33,6 +89,54 @@ wheels = [
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+[[package]]
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+version = "3.4.2"
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