{"id":44221,"library":"aicsimageio","title":"AICSImageIO","description":"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.","status":"active","version":"4.14.0","language":"python","source_language":"en","source_url":"https://github.com/AllenCellModeling/aicsimageio","tags":["microscopy","imageIO","ome-tiff","czi"],"install":[{"cmd":"pip install aicsimageio","lang":"bash","label":"base"},{"cmd":"pip install aicsimageio[czi]","lang":"bash","label":"with CZI extra"},{"cmd":"pip install aicsimageio[bioformats]","lang":"bash","label":"with bioformats extra"}],"dependencies":[{"reason":"core dependency for lazy reading","package":"dask","optional":false},{"reason":"return type for image data","package":"xarray","optional":false},{"reason":"image arrays","package":"numpy","optional":false}],"imports":[{"note":"AICSImage is accessible from the top-level package, not from readers submodule.","wrong":"from aicsimageio.readers import AICSImage","symbol":"AICSImage","correct":"from aicsimageio import AICSImage"},{"note":"Reader classes are in the readers submodule, not the top level.","wrong":"from aicsimageio import CziReader","symbol":"readers","correct":"from aicsimageio.readers import CziReader, OmeTiffReader"},{"note":"Writers are in a separate submodule.","wrong":"","symbol":"writers","correct":"from aicsimageio.writers import OmeTiffWriter"}],"quickstart":{"code":"from aicsimageio import AICSImage\n\n# Read an image file (supports many formats)\nimg = AICSImage(\"example.czi\")\nprint(f\"Shape: {img.dims.shape}\")  # returns tuple like (C, Z, T, Y, X)\n\n# Get numpy array (loads into memory)\ndata = img.get_image_dask_data().compute()\nprint(f\"Data shape: {data.shape}\")\n\n# Get metadata\nprint(img.metadata)\n","lang":"python","description":"Opens a microscopy image file, shows dimensions, reads data as a dask array, and prints metadata."},"warnings":[{"fix":"Use `from aicsimageio import AICSImage`.","message":"In 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.","severity":"breaking","affected_versions":">=4.0"},{"fix":"Use `img.get_image_dask_data().compute()` to get a numpy array.","message":"The `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.","severity":"deprecated","affected_versions":">=4.0"},{"fix":"Print `img.dims.shape` and `img.dims.order` to understand the ordering before slicing.","message":"Dimensions 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.","severity":"gotcha","affected_versions":"all"},{"fix":"Install with the appropriate extra: `pip install aicsimageio[czi]` or `pip install aicsimageio[all]`.","message":"Some 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`.","severity":"gotcha","affected_versions":"all"}],"env_vars":null,"search_vec":"'3.9':23 '4.14.0':20 'aicsimageio':1,2 'allen':45 'bsd':54 'cell':48 'convert':13 'czi':34,61 'data':16 'develop':42 'e.g':33 'file':31 'format':32 'imag':15 'imageio':57 'institut':46 'interfac':28 'librari':8 'licens':55 'lif':38 'metadata':18 'microscopi':14,56 'nd2':39 'numer':30 'ome':36,59 'ome-tiff':35,58 'provid':25 'pure':6 'pure-python':5 'python':7,22 'read':10 'releas':51 'scienc':49 'support':21 'tiff':37,60 'unifi':27 'version':19 'write':11","created_at":"2026-06-07T12:49:03.667146+00:00","updated_at":"2026-06-07T12:49:03.667146+00:00","problems":[{"fix":"Change import to `from aicsimageio import AICSImage`.","cause":"Breaking change in version 4.0: AICSImage moved to top-level package.","error":"ImportError: cannot import name 'AICSImage' from 'aicsimageio.readers'"},{"fix":"Install the appropriate extra, e.g., `pip install aicsimageio[czi]` for .czi files.","cause":"Missing optional dependency for the file format (e.g., CZI, LIF).","error":"aicsimageio.exceptions.UnsupportedFileFormatError: No readers found for file ..."},{"fix":"Use `img.get_image_dask_data()[0, :, :].compute()` or use `img.get_image_data(...)` with specific dimensions.","cause":"Trying to index the AICSImage object directly like an array (e.g., img[0, :, :]). AICSImage is not array-like.","error":"TypeError: 'AICSImage' object does not support indexing"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"quickstart_score":null,"quickstart_tag":null,"pypi_latest":null,"cli_name":null,"cli_version":null,"type":"library","homepage":"https://github.com/AllenCellModeling/aicsimageio","github":"https://github.com/AllenCellModeling/aicsimageio","docs":null,"changelog":null,"pypi":null,"npm":null,"openapi_spec":null,"status_page":null,"smithery":null,"categories":["devops"],"base_url":null,"auth_type":null,"provenance":{"verified_status":"passing","verified_at":"2026-06-29","last_verified":"2026-06-29","next_check":"2026-07-29","install_tag":null}}