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Changelog

[0.5.3]

Fix

  • Fix bug in AnnData backend where "raw" entry with encoding-type "null" is written by default in newer anndata versions, which causes compatibility issues with older anndata versions. Now the "raw" entry is removed after writing if it has encoding-type "null".

[0.5.2]

Fix

  • Fix critical bug in masking roi image handling causing incorrect results when image and mask have different pixel sizes.
  • Fix bug in loading masking roi images when paths other than default are used.

[0.5.1]

Fix

  • Fix bug causing incorrect channel metadata when creating an image.
  • Fix correctly setting the space and time units when creating an image.
  • Fix minor bug in set_channel_windows_with_percentiles method.

Chores

  • Improve logging consistency across the codebase.

[v0.5.0]

Features

  • Add support for OME-NGFF v0.5
  • Move to zarr-python v3
  • API to delete labels and tables from OME-Zarr containers and HCS plates.
  • Allow to explicitly set axes order when building masking roi tables.
  • New metadata modification APIs for Image, Label, and OmeZarrContainer:
  • set_channel_labels - Update channel labels
  • set_channel_colors - Update channel colors
  • set_channel_windows - Update channel display windows (start/end values)
  • set_channel_windows_with_percentiles - Update display windows based on data percentiles
  • set_axes_names - Rename axes in the metadata
  • set_axes_unit - Set space and time units for axes
  • set_name - Set the image/label name in metadata
  • Add translation support in all image/label creation and derivation APIs.

API Breaking Changes

  • New Roi models, now supporting arbitrary axes.
  • The compressor argument has been renamed to compressors in all relevant functions and methods to reflect the support for multiple compressors in zarr v3.
  • The version argument has been renamed to ngff_version in all relevant functions and methods to specify the OME-NGFF version.
  • Remove the parallel_safe argument from all zarr related functions and methods. The locking mechanism is now handled internally and only depends on the cache.
  • Remove the unused parent argument from ZarrGroupHandler.
  • Internal changes to ZarrGroupHandler to support cleanup unused apis.
  • Remove ngio_logger in favor of standard warnings module.

Migration Guide (v0.4 → v0.5)

Roi API Changes

The Roi class now uses a flexible slice-based model supporting arbitrary axes:

# Old (v0.4)
roi = Roi(x=34.1, y=10, x_length=321.6, y_length=330)

# New (v0.5)
roi = Roi.from_values(slices={"x": (34.1, 321.6), "y": (10, 330)}, name=None)

# Accessing coordinates
# Old: roi.x, roi.y, roi.x_length, roi.y_length
# New: roi.get("x").start, roi.get("y").start, roi.get("x").length, roi.get("y").length

Argument Renames

# compressor → compressors
# Old (v0.4)
create_empty_ome_zarr(..., compressor=Blosc())

# New (v0.5)
create_empty_ome_zarr(..., compressors=Blosc())

# version → ngff_version
# Old (v0.4)
create_empty_ome_zarr(..., version="0.4")

# New (v0.5)
create_empty_ome_zarr(..., ngff_version="0.4")

Removed Arguments

  • parallel_safe: No longer needed, locking is handled internally
  • ngio_logger: Use Python's standard warnings module instead

Deprecations

  • Standardized all deprecation warnings to indicate removal in ngio=0.6.
  • Deprecated set_channel_percentiles method, use set_channel_windows_with_percentiles instead.

Bug Fixes

  • Fix bug in consolidate function when using coarsening mode with non power-of-two shapes.
  • Fix HCS plate column name formatting to use standardized zero-padding (e.g., column 3 is now stored as "03").
  • Fix _stringify_column not passing num_digits parameter to _format_int_column.

Documentation

  • Fix incorrect and incomplete docstrings across the codebase:
  • compute_masking_roi: Added Args/Returns, fixed description (supports 2D, 3D, 4D).
  • lazy_compute_slices: Added Args/Returns sections.
  • LabelsContainer.list: Fixed description (was "Create the /labels group").
  • build_masking_roi_table: Added Args/Returns sections.
  • TablesContainer: Fixed class and method descriptions (were referencing labels instead of tables).
  • NgioPlateMeta.add_well: Fixed description (was "Add an image to the well").
  • NgioPlateMeta.derive: Fixed type annotation in docstring (NgffVersion → NgffVersions).
  • Added missing docstrings to several HCS helper functions.

[v0.4.7]

Bug Fixes

  • Fix bug adding time axis to masking roi tables.

Bug Fixes

  • Fix channel selection from wavelength_id
  • Fix table opening mode to stop wrtiting groups when opening in append mode.

[v0.4.5]

Bug Fixes

  • Pin Dask to version <2025.11 to avoid errors when writing zarr pyramids with dask (see https://github.com/dask/dask/issues/12159#issuecomment-3548421833)

[v0.4.4]

Bug Fixes

  • Fix bug in channel visualization when using hex colors with leading '#'.
  • Remove strict range check in channel window.

[v0.4.3]

Bug Fixes

  • Fix bug in deriving labels and image from OME-Zarr with non standard path names.
  • Add missing pillow dependency.
  • Update pixi workspace config.

[v0.4.2]

API Changes

  • Make roi.to_slicing_dict(pixel_size) always require pixel_size argument for consistency with other roi methods.
  • Make PixelSize object a Pydantic model to allow for serialization.

Bug Fixes

  • Improve robustness when rounding Rois to pixel coordinates.

[v0.4.1]

Bug Fixes

  • Fix bug in zoom transform when input axes contain unknown axes (e.g. virtual axes). Now unknown axes are treated as virtual axes and set to 1 in the target shape.

[v0.4.0]

Features

  • Add Iterators for image processing pipelines
  • Add support for time in rois and roi-tables
  • Building masking roi tables expanded to time series data
  • Add zoom transformation
  • Add support for rescaling on-the-fly masks for masked images
  • Big refactor of the io pipeline to support iterators and lazy loading
  • Add support for customize dimension separators and compression codecs
  • Simplify AxesHandler and Dataset Classes

API Changes

  • The image-like get_* api have been slightly changed. Now if a single int is passed as slice_kwargs, it is interpreted as a single index. So the dimension is automatically squeezed.
  • Remove the get_*_delayed methods, now data cam only be loaded as numpy or dask array.Use the get_as_dask method instead, which returns a dask array that can be used with dask delayed.
  • A new model for channel selection is available. Now channels can be selected by name, index or with ChannelSelectionModel object.
  • Change table_name keyword argument to name for consistency in all table concatenation functions, e.g. concatenate_image_tables, concatenate_image_tables_as, etc.
  • Change to Dimension class. get_shape and get_canonical_shape have been removed, get uses new keyword arguments default instead of strict.
  • Image like objects now have a more clean API to load data. Instead of get_array and set_array, they now use get_as_numpy, and get_as_dask for delayed arrays.
  • Also for get_roi now specific methods are available. For ROI objects, the get_roi_as_numpy, and get_roi_as_dask methods.
  • Table ops moved to ngio.images
  • int label as an explicit attribute in Roi objects (previously only in stored in name and relying on convention)
  • Slight changes to Image and Label objects. Some minor attributes have been renamed for consistency.

Table specs

  • Add t_second and len_t_second to ROI tables and masking ROI tables

[v0.3.5]

  • Remove path normalization for images in wells. While the spec requires paths to be alphanumeric, this patch removes the normalization to allow for arbitrary image paths.

[v0.3.4]

  • allow to write as anndata_v1 for backward compatibility with older ngio versions.

[v0.3.3]

Chores

  • improve dataset download process and streamline the CI workflows

[v0.3.2]

API Changes

  • change table backend default to anndata_v1 for backward compatibility. This will be chaanged again when ngio v0.2.x is no longer supported.

Bug Fixes

  • fix #13 (converters tools)
  • fix #88