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Attempting to load the following dataset from s3 (`s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.zarr/em/fibsem-uint16/`) causes the ome-zarr bdv plugin to fail. Unfortunately the plugin doesn't r…
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**NB** This workflow has been moved to https://github.com/IDR/mkngff_upgrade_scripts (main README)
Once a submission has been processed by BioStudies, it will become available at a URL like:
…
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### Zarr version
2.18.1
### Numcodecs version
0.12.1
### Python Version
3.10.14
### Operating System
Linux
### Installation
From autogenerated from git tag tar ball.
### Description
Looks l…
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See https://github.com/ome/omero-cli-zarr/pull/82#issuecomment-940179664
Currently, if all masks have no Z or T index, the `omero zarr masks Image:ID` exports a label data block with size-Z or size…
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Do we use fixed down-sampling factors?
That's not ideal when the input data is very anisotropic.
It would probably be better to first only downsample the lowest resolution dimension.
Not sure...
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Taking the output of `bioformat2raw 0.3.0` which is a collection of OME-Zarr multiscale images as an example:
```bash
bioformats2raw "test&series=2.fake" "test.zarr"
(zarr) [sbesson@pilot-zarr1-…
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Hey Jeremy, in #238 you mentioned:
> However, Neuroglancer currently only supports that if the dimension is unchunked, i.e. the chunk size is equal to the full extent of the dimension; for your exa…
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What do you think of having the MDA function automatically handle the writing of data to a zarr on disk that conforms to https://ngff.openmicroscopy.org/latest/ ?
I looked into this a little bit bu…
ianhi updated
2 years ago
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**User story**
```[tasklist]
### Tasks
- [x] Shapes - circles (with fixed radius)
- [ ] Shapes - circles with radius column
- [ ] [Shapes - polygons](https://github.com/vitessce/vitessce/issues…
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Workflow:
1. Convert the ``...downloads.openmicroscopy.org/images/OME-TIFF/2016-06/binaryonly`` images into zarr using bf2raw version 0.4.0, using the command
2. ``bioformats2raw binaryonly/multi…