ome-types

library0.6.3pypypi✓ verified 84d ago

Python dataclasses for the OME (Open Microscopy Environment) data model. Provides type-annotated Python objects for OME-XML metadata, enabling type-safe construction and serialization of OME metadata. Current version 0.6.3, supports Python >=3.9. Maintained by tlambert03, regular releases.

serialization data

pip install ome-types

github ↗package ↗docs ↗

INSTALL

IMPORT

SIG · OME-TYPES

ome-types

serializationpythonv0.6.3

Install

3.5s avg

Import

1371ms

Disk

31MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.6.3 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 1.408s · 33.2MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 3.5s · import 1.334s · 33MB

31MB installed

● package 31MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

OME

✓ from ome_types import OME

Image

✓ from ome_types.model import Image

Pixels

✓ from ome_types.model import Pixels

OME as model

✓ from ome_types.model import OME

✗ from ome_types import OME (this is also correct for the top-level OME, but if you want the model specifically use the model submodule)

Both imports work for OME, but model submodule is explicit for internal model classes.

Create an OME object programmatically with required fields and serialize to XML.

from ome_types import OME from ome_types.model import Image, Pixels # Create minimal OME object ome = OME(images=[Image(id='Image:0', name='test', pixels=Pixels(id='Pixels:0', dimension_order='XYZCT', size_x=10, size_y=10, size_c=1, size_z=1, size_t=1, type='uint8'))]) print(ome.to_xml())

Debug

Known issues

gotchaOME model fields are validated at construction; missing required fields raise pydantic ValidationError. Always check required fields (e.g., id, dimension_order, size_x, etc.) for Images and Pixels.

fix

Refer to OME schema documentation for required attributes. Use pydantic's model_dump(mode='python') to debug.

affects: all

deprecatedIn version 0.6.0, the OME class was moved from ome_types.model to ome_types directly. Importing from the old path still works but may be deprecated.

fix

Use 'from ome_types import OME' instead of 'from ome_types.model import OME'.

affects: >=0.6.0

gotchaSerializing to XML with to_xml() will produce a string with default namespaces. If you need custom namespaces or formatting, use to_xml(nsmap=...) but those are not fully documented.

fix

Read the source or use the underlying pydantic XML serialization if needed.

affects: all

gotchaWhen parsing XML with from_xml(), ensure the XML is valid OME-XML. Invalid XML raises ParseError without clear message. Use lxml's parser for better error messages.

fix

Use lxml.etree.parse() to validate XML before passing to from_xml().

affects: all

Errors

Common errors & fixes

pydantic_core._pydantic_core.ValidationError: 1 validation error for OME

Missing required field when constructing OME or model objects.

fix

Check all required fields in the OME schema. For OME object, images is required (list of Image). For Image, id and name are required. For Pixels, id, dimension_order, size_x, size_y, size_c, size_z, size_t, type are required.

ModuleNotFoundError: No module named 'ome_types.model.OME'

Trying to import OME from wrong submodule; in older versions OME was in ome_types.model, newer versions it is in ome_types directly.

fix

Use 'from ome_types import OME' (top-level import) for current versions (>=0.6.0).

AttributeError: 'dict' object has no attribute 'to_xml'

Calling to_xml() on a dict instead of an OME model instance, often happens when using .model_dump() incorrectly.

fix

Ensure you have an OME object, not a dict. Use .model_dump(mode='python') to get dict representation, but to_xml() is only on the model object.

Upgrade

Version history

0.6.3latest on PyPI · released Nov 26, 2025

Audit

Dependencies

pydanticrequiredome-types uses pydantic BaseModel for its dataclasses, required for validation and serialization.

Agent activity

16 hits · last 30 days

node

Resources

githubhttps://github.com/tlambert03/ome-types ↗

packagehttps://pypi.org/project/ome-types/ ↗

docshttps://ome-types.readthedocs.io/en/latest/ ↗