Prepare CZI ZebraFish LSM data

[anwai98]

Hi @schilling40 and @constantinpape,

Here's the data loading heuristics for the data from Loic's group!

I haven't integrated the tracking annotations info but if we are interested in comparisons, I can check it out later!

PS. I didn't see a dev branch so I created this PR on master.

[constantinpape]

I haven't integrated the tracking annotations info but if we are interested in comparisons, I can check it out later!

It makes sense to also add this, we can use it for validating the segmentations based on the same logic we have for validating manual annotations.

PS. I didn't see a dev branch so I created this PR on master.

Yep, that's fine.

[anwai98]

It makes sense to also add this, we can use it for validating the segmentations based on the same logic we have for validating manual annotations.

Solid, thanks @constantinpape!
I will find sometime tomorrow and sort this out!

(meanwhile, I'll keep the PR open and continue working here)

[anwai98]

Well I realized I spoke too early @constantinpape

Turns out, data in the ZebraHub project does have tracking annotations ;) (from this paper: https://doi.org/10.1016/j.cell.2024.09.047)

I managed to get the data and the tracking annotations, and prepared a data fetcher here!

[anwai98]

Okay I added suggestions for 3 time points in the code as comments, all sort of at the end of cycle.

I like the 740 timepoint most because of the illumination / development trade-off at the extreme end-corners on both sides of the embryo!

cc: @constantinpape

[constantinpape]

Thanks @anwai98 . I changed the timepoint accordingly and will merge once the tests pass.