search

fmi-faim / faim-ipa

A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
BSD 3-Clause "New" or "Revised" License
9 stars 6 forks source link

Labelling of row/column in HCS #130

Closed jeskowagner closed 6 months ago

jeskowagner commented 6 months ago

Hi! When working with HCS data, I was wondering whether you had found good way to integrate well (i.e. row/column) information in ome-zarr files when viewed with napari-ome-zarr. It would be great to have information available as to which well a user is looking at, e.g. when hovering their mouse over a cell. I recognise you are not responsible for for napari-ome-zarr, but was just curious whether you had played around with anything in that area from a user perspective. Thanks, Jesko

tibuch commented 6 months ago

Hi Jesko,

We are using MoBIE for ome-zarr plate visualization. It comes with the well ID feature built in and even allows to attach arbitrary tables (e.g. conditions).

Cheers

jeskowagner commented 6 months ago

Amazing, thanks a lot!

jeskowagner commented 6 months ago

Would you happen to have any example zarrs that can be visualised in MoBIE? I have been struggling with errors regarding the multiscale attribute (see here) but would love to see a working example.

tibuch commented 6 months ago

The zarr created by the Single-Plane example should work with MoBIE > Open > Open HCS Dataset.

image

I think it fails if you have trailing / after .zarr.

jeskowagner commented 6 months ago

In case anyone comes across this issue in the future, I resolved the issue relating to multiscales by opening the files with the "Open HCS Dataset" option as detailed here.