webknossos-libs

webknossos-libs copied to clipboard

Writing a small data shape to a compressed Zarr3 array seems to be significantly slower than for WKW: ``` Writing shape (24, 24, 24) to zarr3 mag... took 2.5s Writing...

fm3

## Context Conversion of tiff datasets to wkw (or zarr). ## Expected Behavior Converting one 3D tiff should output a 3D dataset. ## Current Behavior Converting one 3D tiff outputs...

philippotto

[question] how to provide a conda environment for scheduling SLURM jobs with cluster_tools?

1

## Detailed Description - Affected library: cluster_tools I am trying to use cluster_tools to schedule SLURM jobs: My code looks like this: ``` from cluster_tools import SlurmExecutor with SlurmExecutor(job_resources=slurm_settings_dict) as...

neuronflow

## Detailed Description Some jobs that we run on a Slurm cluster (e.g. downsampling) take longer to queue than to actually run. Splitting it up in many small Slurm jobs...

normanrz

Conversion job 6516f962010000cd03861817 of a tiff file failed with this stack trace ``` File "/usr/local/lib/python3.11/site-packages/webknossos/dataset/_utils/pims_images.py", line 495, in copy_to_view with self._open_images() as images: File "/usr/local/lib/python3.11/contextlib.py", line 137, in __enter__ return...

fm3

## Context - Affected library: webknossos The error occurs when creating a Dataset that contains an empty layer using the WK python library and subsequently calling `dataset.upload()`. Code to reproduce...

cdfhalle

Don’t Include Data Outside of Bounding Box in Downsampling Interpolation

1

When downsampling data with interpolation, it would be helpful to have an option to exclude data outside of the dataset bounding box. In case of very thin datasets (my example...

fm3

Should probably be supported by bioformats (?) compare https://scm.slack.com/archives/C5AKLAV0B/p1689600583314559?thread_ts=1689579012.878959&cid=C5AKLAV0B

fm3

When opening a remote dataset, the supplied `webknossos_url` is compared to the active webknossos context's url. If only one of the two has a trailing slash, the comparison fails and...

daniel-wer

Downloading annotation layer with Python library, but downloaded annotation is not the same size as the actual image layer?

4

Hello, I've been using the following code to programmatically download our annotations from our WebKnossos instance. However, I've run into an issue, where the size of the downloaded annotation cutout...

azatian