Accessing Airyscan Raw Data

[Omnistic]

Feature Description

I was trying to read an unprocessed CZI file from a Airyscan unit. In Fiji, I can open said image and the dimensions are as follows:

• For each acquisition channels, there are two color channels
• In the first color channel there are 32 time points, and I think each time point is the raw data from an individual Airyscan detector
• In the second color channel, only the first time point has data (other 31 time points are all zeros), and I think it is the sum of all individual detectors

When I read the same image with bioio, I get:
<Dimensions [T: 1, C: 6, Z: 1, Y: 1119, X: 1119]>

I tried with and without:
use_aicspylibczi=True

I can get the expected 6 color channels (I have 3 acquisition channel), but there's only one time point.

As much as I searched, I couldn't find how to properly get Airyscan raw data in Python and I am using Fiji as a workaround for now.

Thank you for your consideration and apologies if I missed an obvious way to do what I want.

Use Case

If you can acquire Airyscan data, Zeiss will provide a method to process this data in their software (ZEN). However, they still provide access to the raw data giving the community an opportunity to have an open-source processing of Airyscan data.

Solution

The T dimension should be 32 (the number of airyscan individual detectors).

Here is the test image I was using: https://zenodo.org/records/17423258

Alternatives

Use Fiji (potentially with a macro) to extract this data before using it with Python.