Skip to content

Add legacy STK support#125

Draft
jeskowagner wants to merge 9 commits into
fmi-faim:mainfrom
jeskowagner:legacy_stk
Draft

Add legacy STK support#125
jeskowagner wants to merge 9 commits into
fmi-faim:mainfrom
jeskowagner:legacy_stk

Conversation

@jeskowagner

Copy link
Copy Markdown
Contributor

Enabled by the great refactoring of faim-hcs to faim-ipa, #18 can now be tackled. This PR hijacks metadata extraction of metaseries created with ImageXpress to enable users to feed legacy STK-formatted tif files seamlessly. However, this approach currently only support single-plane acquisitions (in this line) simply because I do not have access to multi-plane acquisitions to test any other format.

I am marking this as draft PR because

  • it hijacks metaseries extraction (and thus the function name is misleading if used for STK's)
  • I cannot extensively test it without more diverse STK data

Beyond that it seems to work as expected, producing valid zarr files.

@jeskowagner

jeskowagner commented May 3, 2024

Copy link
Copy Markdown
Contributor Author

I just noticed that this was also enabled by the tifffile package adding better metadata extraction support for STK's, without which the StagePosition field is not populated (which is needed by faim-ipa). Specifically, the required PR was this. Very cool to see others working to push what can be done with these legacy files. Note that this PR also suggests that getting this metadata is supported for single-plane STK's only, so this limitation would likely be insurmountable.

@imagejan imagejan self-assigned this May 3, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants