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Ome writer output #200

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520b154
use ome-writer with acquire-zarr backend instead of acquire-zarr dire…
jeskesen Aug 29, 2025
93c8313
since mm-app-path & ls-config-path are optional, don't fail if the fi…
jeskesen Sep 2, 2025
3e591f3
style
jeskesen Sep 2, 2025
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131 changes: 64 additions & 67 deletions mantis/acquisition/acq_engine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from threading import Thread
from typing import Iterable, Union

import acquire_zarr as aqz
from ome_writers import create_stream, Dimension
import copylot
import nidaqmx
import numpy as np
Expand Down Expand Up @@ -220,7 +220,12 @@ def autoexposure_settings(self, settings: AutoexposureSettings):
)
self._autoexposure_settings = settings

def setup(self, output_path: Union[str, os.PathLike] = None):
def setup(
self,
output_path: Union[str, os.PathLike] = None,
position_settings=None,
time_settings=None,
):
"""
Apply acquisition settings as specified by the class properties
"""
Expand Down Expand Up @@ -285,57 +290,41 @@ def setup(self, output_path: Union[str, os.PathLike] = None):
y_size = self.mmc.getImageHeight()

if output_path:
zarr_settings = aqz.StreamSettings(
store_path=output_path,
dtype=aqz.DataType.UINT16, # FIXME: hardcoded for now, should be set from acquisition settings
dimensions=[
aqz.Dimension(
name='t',
array_size_px=0,
chunk_size_px=1,
shard_size_chunks=1,
kind=aqz.DimensionType.TIME,
), # zero denotes the append dimension in acquire
aqz.Dimension(
name='z',
array_size_px=self.slice_settings.num_slices,
chunk_size_px=int(self.slice_settings.num_slices / z_n_chunks),
shard_size_chunks=1,
kind=aqz.DimensionType.SPACE,
),
aqz.Dimension(
name='y',
array_size_px=y_size,
chunk_size_px=int(y_size / xy_n_chunks),
shard_size_chunks=1,
kind=aqz.DimensionType.SPACE,
),
aqz.Dimension(
name='x',
array_size_px=x_size,
chunk_size_px=int(x_size / xy_n_chunks),
shard_size_chunks=1,
kind=aqz.DimensionType.SPACE,
),
],
muiltscale=False,
version=aqz.ZarrVersion.V3,
max_threads=0,
# Create dimensions for ome_writers with position and time dimensions
num_positions = position_settings.num_positions if position_settings else 1
num_timepoints = time_settings.num_timepoints if time_settings else 1

dimensions = [
Dimension(
label='p', size=num_positions, chunk_size=1 # position dimension
),
Dimension(label='t', size=num_timepoints, chunk_size=1), # time dimension
Dimension(
label='c',
size=self.channel_settings.num_channels,
chunk_size=self.channel_settings.num_channels,
),
Dimension(
label='z',
size=self.slice_settings.num_slices,
chunk_size=int(max(1, self.slice_settings.num_slices / z_n_chunks)),
),
Dimension(
label='y', size=y_size, chunk_size=int(max(1, y_size / xy_n_chunks))
),
Dimension(
label='x', size=x_size, chunk_size=int(max(1, x_size / xy_n_chunks))
),
]

self._ome_writer = create_stream(
output_path,
dtype='uint16', # FIXME: hardcoded for now, should be set from acquisition settings
dimensions=dimensions,
backend="acquire-zarr",
overwrite=True,
)

if self.channel_settings.num_channels > 1:
zarr_settings.dimensions.insert(
1,
aqz.Dimension(
name='c',
array_size_px=self.channel_settings.num_channels,
chunk_size_px=int(self.channel_settings.num_channels),
shard_size_chunks=1,
kind=aqz.DimensionType.CHANNEL,
),
)
self._zarr_writer = aqz.ZarrStream(zarr_settings)

self.mmc.mda.events.frameReady.connect(self.write_data)

def reset(self):
Expand Down Expand Up @@ -388,7 +377,7 @@ def write_data(self, data: np.ndarray, event: useq.MDAEvent) -> None:
event : useq.Event
The event containing metadata about the acquisition.
"""
self._zarr_writer.append(data)
self._ome_writer.append(data)


class MantisAcquisition(object):
Expand Down Expand Up @@ -836,19 +825,19 @@ def setup_autoexposure(self):
)
if ts2_ttl_state == 32:
# State 32 corresponds to illumination with 488 laser
self.ls_acq.channel_settings.light_sources[
channel_idx
] = microscope_operations.setup_vortran_laser(VORTRAN_488_COM_PORT)
self.ls_acq.channel_settings.light_sources[channel_idx] = (
microscope_operations.setup_vortran_laser(VORTRAN_488_COM_PORT)
)
elif ts2_ttl_state == 64:
# State 64 corresponds to illumination with 561 laser
self.ls_acq.channel_settings.light_sources[
channel_idx
] = microscope_operations.setup_vortran_laser(VORTRAN_561_COM_PORT)
self.ls_acq.channel_settings.light_sources[channel_idx] = (
microscope_operations.setup_vortran_laser(VORTRAN_561_COM_PORT)
)
elif ts2_ttl_state == 128:
# State 128 corresponds to illumination with 639 laser
self.ls_acq.channel_settings.light_sources[
channel_idx
] = microscope_operations.setup_vortran_laser(VORTRAN_639_COM_PORT)
self.ls_acq.channel_settings.light_sources[channel_idx] = (
microscope_operations.setup_vortran_laser(VORTRAN_639_COM_PORT)
)
else:
logger.error(
'Unknown TTL state {} for channel {} in config group {}'.format(
Expand Down Expand Up @@ -1195,10 +1184,18 @@ def setup(self):
logger.info('Setting up acquisition')

logger.debug('Setting up label-free acquisition')
self.lf_acq.setup(output_path=f'{self._acq_dir}/{self._acq_name}_{LF_ACQ_LABEL}')
self.lf_acq.setup(
output_path=f'{self._acq_dir}/{self._acq_name}_{LF_ACQ_LABEL}',
position_settings=self.position_settings,
time_settings=self.time_settings,
)

logger.debug('Setting up light-sheet acquisition')
self.ls_acq.setup(output_path=f'{self._acq_dir}/{self._acq_name}_{LS_ACQ_LABEL}')
self.ls_acq.setup(
output_path=f'{self._acq_dir}/{self._acq_name}_{LS_ACQ_LABEL}',
position_settings=self.position_settings,
time_settings=self.time_settings,
)

logger.debug('Setting up DAQ')
self.setup_daq()
Expand Down Expand Up @@ -1299,10 +1296,10 @@ def acquire(self):
)
continue
else:
self.position_settings.xyz_positions[p_idx][
2
] = self.lf_acq.mmc.getPosition(
self.lf_acq.microscope_settings.autofocus_stage
self.position_settings.xyz_positions[p_idx][2] = (
self.lf_acq.mmc.getPosition(
self.lf_acq.microscope_settings.autofocus_stage
)
)
logger.debug(
f'Autofocus successful. Z position updated to {self.position_settings.xyz_positions[p_idx][2]} at position {p_label}'
Expand Down
4 changes: 2 additions & 2 deletions mantis/cli/run_acquisition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,15 +26,15 @@ def load_settings(raw_settings: dict, settings_key: str, settings_class):
@click.option(
"--mm-app-path",
default=default_mm_app_path,
type=click.Path(exists=True, file_okay=False, dir_okay=True),
type=click.Path(file_okay=False, dir_okay=True),
show_default=True,
help='''Path to Micro-manager installation directory
which will run the light-sheet acquisition''',
)
@click.option(
"--ls-config-filepath",
default=default_ls_config_filepath,
type=click.Path(exists=True, file_okay=True, dir_okay=False),
type=click.Path(file_okay=True, dir_okay=False),
show_default=True,
help='''Path to Micro-manager config file
which will run the light-sheet acquisition''',
Expand Down
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