aicsimageio

library4.14.0pypypi✓ verified 84d ago

AICSImageIO is a pure-Python library for reading, writing, and converting microscopy image data and metadata. Version 4.14.0 supports Python >=3.9 and provides a unified interface for numerous file formats (e.g., CZI, OME-TIFF, LIF, ND2). It is developed by the Allen Institute for Cell Science and released under a BSD license.

devops

pip install aicsimageio

github ↗homepage ↗

INSTALL

IMPORT

SIG · AICSIMAGEIO

aicsimageio

devopspythonv4.14.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

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

AICSImage

✓ from aicsimageio import AICSImage

✗ from aicsimageio.readers import AICSImage

AICSImage is accessible from the top-level package, not from readers submodule.

readers

✓ from aicsimageio.readers import CziReader, OmeTiffReader

✗ from aicsimageio import CziReader

Reader classes are in the readers submodule, not the top level.

writers

✓ from aicsimageio.writers import OmeTiffWriter

Writers are in a separate submodule.

Opens a microscopy image file, shows dimensions, reads data as a dask array, and prints metadata.

from aicsimageio import AICSImage # Read an image file (supports many formats) img = AICSImage("example.czi") print(f"Shape: {img.dims.shape}") # returns tuple like (C, Z, T, Y, X) # Get numpy array (loads into memory) data = img.get_image_dask_data().compute() print(f"Data shape: {data.shape}") # Get metadata print(img.metadata)

Debug

Known issues

breakingIn version 4.0, the `AICSImage` class moved from the `readers` submodule to the top-level package. Importing from `aicsimageio.readers.AICSImage` will raise an ImportError.

fix

Use `from aicsimageio import AICSImage`.

affects: >=4.0

deprecatedThe `img.data` property (numpy array) is deprecated in favor of `img.get_image_dask_data()` to emphasize lazy loading. `img.data` may be removed in future versions.

fix

Use `img.get_image_dask_data().compute()` to get a numpy array.

affects: >=4.0

gotchaDimensions order varies by file format. The default returned by `img.dims.order` may not match expectations (e.g., CZI uses ['C', 'Z', 'T', 'S', 'Y', 'X'] while OME-TIFF uses ['T', 'C', 'Z', 'Y', 'X']). Always check dims before accessing indices.

fix

Print `img.dims.shape` and `img.dims.order` to understand the ordering before slicing.

affects: all

gotchaSome file formats require extra dependencies. For example, CZI files need `aicsimageio[czi]` which installs `czifile` and `pylibtiff`. Without it, opening a .czi file raises an `UnsupportedFileFormatError`.

fix

Install with the appropriate extra: `pip install aicsimageio[czi]` or `pip install aicsimageio[all]`.

affects: all

Errors

Common errors & fixes

ImportError: cannot import name 'AICSImage' from 'aicsimageio.readers'

Breaking change in version 4.0: AICSImage moved to top-level package.

fix

Change import to `from aicsimageio import AICSImage`.

aicsimageio.exceptions.UnsupportedFileFormatError: No readers found for file ...

Missing optional dependency for the file format (e.g., CZI, LIF).

fix

Install the appropriate extra, e.g., `pip install aicsimageio[czi]` for .czi files.

TypeError: 'AICSImage' object does not support indexing

Trying to index the AICSImage object directly like an array (e.g., img[0, :, :]). AICSImage is not array-like.

fix

Use `img.get_image_dask_data()[0, :, :].compute()` or use `img.get_image_data(...)` with specific dimensions.

Upgrade

Version history

4.14.0latest on PyPI · released Nov 1, 2023

Audit

Dependencies

daskrequiredcore dependency for lazy reading

xarrayrequiredreturn type for image data

numpyrequiredimage arrays

Agent activity

30 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/AllenCellModeling/aicsimageio ↗

homepagehttps://github.com/AllenCellModeling/aicsimageio ↗