function to convert Zeiss .czi files to DeepZoom .dzi using aicsimageio and pyvips

[rcasero]

Hi,

I've written a little function to convert Zeiss .czi files to DeepZoom .dzi using aicsimageio and pyvips (in my case, my interest is to be able to visualise them in the web browser application AIDA).

https://github.com/MRC-Harwell/cytometer/blob/c96e86c144c63978881330ad8275d10649096fcd/cytometer/data.py#L1525

The functionality is a bit limited to the Zeiss files I'm using now, and there may be a better way to do this, but I thought I'd drop a link here, as maybe somebody else is interested.

[evamaxfield]

Hey @rcasero this is awesome!

We may make an "AICSImageIO Examples" section in documentation and link to this if that is okay! No timeline on that at all just a thought.

Three sidenotes:

1. AICSImage.dims doesn't load any of the image data into memory (or at least it shouldn't...) so you should be able to get the Y and X from the dims object too instead of parsing metadata.
2. If the aim is a perfect conversion from one to another you may want to use AICSImage.reader.data to get all the data and dimensions in the file as the AICSImage object will only pull the "OME standard dimensions".
3. Should we add a DziReader to the library?

[toloudis]

Interesting side note: I used dzi format (in conjunction with lots of aicsimageio processing) to make this visualization with OpenSeaDragon: https://www.allencell.org/deep-cell-zoom.html

[rcasero]

1. AICSImage.dims doesn't load any of the image data into memory (or at least it shouldn't...) so you should be able to get the Y and X from the dims object too instead of parsing metadata.

@JacksonMaxfield That's what I thought, but I have an image with <Dimensions [T: 1, C: 1, Z: 1, Y: 76766, X: 131243, S: 3]>, and doing im.dims takes a good 17min. Details in issue #274.

[rcasero]

2. If the aim is a perfect conversion from one to another you may want to use AICSImage.reader.data to get all the data and dimensions in the file as the AICSImage object will only pull the "OME standard dimensions".

@JacksonMaxfield So far, for my project, I think the standard dimensions work, but I'm happy if somebody wants to improve or reuse my code under the Apache licence.

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