Can't remove series from directory structure with `--scale-format-string`
Closed this issue ยท 4 comments
As suggested in the readme, I am trying to remove the series from the directory structure with the argument --scale-format-string
.
The full command I am using is
bioformats2raw data/Xenium_FFPE_Human_Breast_Cancer_Rep1_morphology_mip.ome.tif data.zarr/images/morphology_mip -p --max-workers 16 --no-root-group --no-ome-meta-export --scale-format-string '%2$d/'
Unfortunately I see that .zattrs
doesn't fill in the path for the multiscale transformations, leading to the inability for napari-ome-zarr
to open the image.
"datasets" : [ {
"path" : "",
"coordinateTransformations" : [ {
"scale" : [ 1.0, 1.0, 1.0, 0.2125, 0.2125 ],
"type" : "scale"
} ]
}, {
"path" : "",
"coordinateTransformations" : [ {
"scale" : [ 1.0, 1.0, 1.0, 0.425, 0.425 ],
"type" : "scale"
} ]
},
...
Thanks, @LucaMarconato. #181 should fix this issue; if you have a chance to test it, we'd welcome any feedback.
@melissalinkert thanks for taking a look at this! I wanted to try out #181 but couldn't install it in dev mode. I could only install it via conda. Could you walk me through the developer installation to check out #181 ?
Thanks!
@giovp : from https://github.com/glencoesoftware/bioformats2raw/pull/181/checks:
- click
Gradle
on the left-hand side - scroll to the bottom of the page and click
bioformats2raw
underArtifacts
. That should download abioformats2raw.zip
file which is a build of bioformats2raw with the changes in #181 - unzip
bioformats2raw.zip
- unzip the extracted
bioformats2raw-0.7.0-SNAPSHOT.zip
- run
bin/bioformats2raw
(with the usual options) from the unzippedbioformats2raw-0.7.0-SNAPSHOT
directory
bin/bioformat2raw --version
should show Version = 0.7.0-SNAPSHOT
, indicating that this is a development build. If any of that doesn't work, just let us know.
fantastic, very useful, it works!
"name" : "Image0",
"datasets" : [ {
"path" : "0",
"coordinateTransformations" : [ {
"scale" : [ 1.0, 1.0, 1.0, 0.2125, 0.2125 ],
"type" : "scale"
} ]
}, {
"path" : "1",
"coordinateTransformations" : [ {
"scale" : [ 1.0, 1.0, 1.0, 0.425, 0.425 ],
"type" : "scale"
} ]
}, {
"path" : "2",
"coordinateTransformations" : [ {
"scale" : [ 1.0, 1.0, 1.0, 0.85, 0.85 ],
"type" : "scale"
} ]
}, {
```