Question 1

Is AICSImageIO still being updated?

Accepted Answer

No, AICSImageIO is in maintenance mode only. The Allen Institute has shifted active development to its successor, bioio, so users should migrate for new features and support.

Question 2

How do I install AICSImageIO for ND2 files?

Accepted Answer

Install with the nd2 extra: pip install aicsimageio[nd2]. This adds the specific dependencies needed to read Nikon ND2 format files in Python.

Question 3

AICSImageIO vs bioio: which one should I use?

Accepted Answer

For new projects, use bioio as it's the actively maintained successor with similar features. AICSImageIO is stable but won't receive updates; bioio offers continued development and improvements.

Question 4

Can AICSImageIO read images from Amazon S3?

Accepted Answer

Yes, with s3fs installed (pip install s3fs), you can read directly from S3 using paths like s3://my-bucket/my-file.tiff, thanks to fsspec integration for cloud storage.

Question 5

How to handle mosaic tiles in LIF files with AICSImageIO?

Accepted Answer

AICSImageIO automatically stitches mosaic tiles for supported formats like LIF. Use AICSImage with reconstruct_mosaic=True (default) for stitched images, or set to False to access individual tiles via the M dimension.

Question 6

What formats can AICSImageIO write to?

Accepted Answer

It primarily writes to OME-TIFF with partial metadata, plus basic formats like PNG via imageio extras. For full format support, writing is more limited compared to reading, focusing on OME-TIFF for microscopy data.

AICSImageIO

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