CZI: Take PixelShift into account

[dominikl]

Probably more a feature request than an issue...

"On the Zeiss Axioscan, during acquisition, there’s an option to shift the pixels of some channels to better align them and remove chromatic aberration. This gets written into the metadata of the .czi file. When opening an image with Fiji/QuPath using Bioformats, this setting is not applied,..."

See image.sc - Bioformats not reading some Zen Axioscan Settings

( Sample file copied to inbox/imagesc-113175 )

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/bioformats-not-reading-some-zen-axioscan-settings/113175/2

[saramcardle]

Here's an example file: https://drive.google.com/file/d/1kwpfu2CSaqMPE26Ae5pO3O1CS0ESlDcG/view?usp=drive_link

[NicoKiaru]

Normally, you don't really need to read the shift from a metadata field. The shift directly appears in the sublock location.

The quick start reader (right) relies on subblock location and handles the shift correctly:

The quick start reader reads the location for each czt from the block start dimension X and Y and is block specific:

https://github.com/BIOP/quick-start-czi-reader/blob/ef156ef5bba92905a4129dac5b231b1f87edeb2c/src/main/java/ch/epfl/biop/formats/in/ZeissQuickStartCZIReader.java#L1020-L1021

In the current default bio-format reader there's a lot of different branches in the openbytes method, so I don't know exactly what would need to be changed.