diff --git a/mantis/acquisition/scripts/measure_psf.py b/mantis/acquisition/scripts/measure_psf.py index 5584f5be..0ba63cdb 100644 --- a/mantis/acquisition/scripts/measure_psf.py +++ b/mantis/acquisition/scripts/measure_psf.py @@ -7,7 +7,7 @@ import numpy as np import torch -from iohub.ngff_meta import TransformationMeta +from iohub.ngff import TransformationMeta from iohub.reader import open_ome_zarr from pycromanager import Acquisition, Core, multi_d_acquisition_events diff --git a/mantis/analysis/scripts/simple_phase_recon.py b/mantis/analysis/scripts/simple_phase_recon.py index 54360191..e22eb3ae 100644 --- a/mantis/analysis/scripts/simple_phase_recon.py +++ b/mantis/analysis/scripts/simple_phase_recon.py @@ -4,7 +4,7 @@ import numpy as np from iohub import open_ome_zarr, read_micromanager -from iohub.ngff_meta import TransformationMeta +from iohub.ngff import TransformationMeta from recOrder.compute.reconstructions import initialize_reconstructor, reconstruct_phase3D # %% Load data diff --git a/mantis/cli/estimate_psf.py b/mantis/cli/estimate_psf.py index 7c99b441..dc31c645 100644 --- a/mantis/cli/estimate_psf.py +++ b/mantis/cli/estimate_psf.py @@ -8,8 +8,7 @@ import numpy as np import torch -from iohub.ngff import open_ome_zarr -from iohub.ngff_meta import TransformationMeta +from iohub.ngff import open_ome_zarr, TransformationMeta from mantis.analysis.AnalysisSettings import PsfFromBeadsSettings from mantis.analysis.analyze_psf import detect_peaks, extract_beads diff --git a/mantis/cli/stitch.py b/mantis/cli/stitch.py index 4d26ff36..78eaa478 100644 --- a/mantis/cli/stitch.py +++ b/mantis/cli/stitch.py @@ -8,8 +8,7 @@ import numpy as np import pandas as pd -from iohub import open_ome_zarr -from iohub.ngff_meta import TransformationMeta +from iohub import open_ome_zarr, TransformationMeta from slurmkit import HAS_SLURM, SlurmParams, slurm_function, submit_function from mantis.analysis.AnalysisSettings import StitchSettings diff --git a/mantis/cli/update_scale_metadata.py b/mantis/cli/update_scale_metadata.py index 0fc19989..7b33c7fc 100644 --- a/mantis/cli/update_scale_metadata.py +++ b/mantis/cli/update_scale_metadata.py @@ -3,7 +3,7 @@ import click from iohub import open_ome_zarr -from iohub.ngff_meta import TransformationMeta +from iohub.ngff import TransformationMeta from mantis.cli.parsing import input_position_dirpaths diff --git a/mantis/cli/utils.py b/mantis/cli/utils.py index d244799e..c7e39388 100644 --- a/mantis/cli/utils.py +++ b/mantis/cli/utils.py @@ -12,8 +12,7 @@ import numpy as np import yaml -from iohub.ngff import Position, open_ome_zarr -from iohub.ngff_meta import TransformationMeta +from iohub.ngff import Position, open_ome_zarr, TransformationMeta from numpy.typing import DTypeLike from tqdm import tqdm