search

ome / ome-ngff-tools

Document available viewers and other tools for the OME-NGFF image format
https://ome.github.io/ome-ngff-tools
BSD 3-Clause "New" or "Revised" License
2 stars 4 forks source link

Mobie #3

Closed jburel closed 2 years ago

jburel commented 2 years ago

Reviewing entries for mobie.

will-moore commented 2 years ago

The Z-downsample image https://minio-dev.openmicroscopy.org/idr/v0.4/idr0077/9836832_z_dtype_fix.zarr in MoBIE is black, but the scalebar is shown:

Screenshot 2022-11-04 at 15 59 20

It has scale: [1 , 1 , 1 , 1] , in the coordinateTransformation of the first dataset, which is also true in the McDole image: https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0044A/4007801.zarr which also shows a scalebar.

However, in other images with floating-point values for scale, https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr shows the scalebar in pixels: Screenshot 2022-11-04 at 14 03 24

will-moore commented 2 years ago

Created new issue for the scalebar, so we could link to that: https://github.com/mobie/mobie-viewer-fiji/issues/894