webknossos-libs

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### Description: - abc ### Issues: - fixes #... ### Todos: Make sure to delete unnecessary points or to check all before merging: - [ ] Updated Changelog - [...

jstriebel

## Detailed Description Affected library: cluster-tools It would be great to have a clear interface, what the cluster-tools executors setup and pass on between different jobs. This should then be...

jstriebel

speed up tests

2

## CLI integration tests Some of the CLI test scripts take quite long and should be sped up (by using a smaller test case, or by improving the routines if...

jstriebel

Allow live compression for tiled cubing

4

philippotto

Support 2d conversion

4

The wkw format is ill-suited for large 2D images. Therefore, webknossos has experimental support for tiled-tiff formats. The cuber should auto-detect 2D input files and convert them to tiled-tiffs including...

normanrz

Save TIFF with compression

1

Would it be possible to provide an option to compress TIFF with ZIP or LZW when using `wkcuber.export_wkw_as_tiff`? This is especially beneficial when exporting segmentation images.

cnzqy1

Trying to cube a multi-page tiff file with `python -m wkcuber --scale 1,2,3 --name myDataset --max_mag 32 /input/path /output/path` (in the directory is a single tiff file with spaces in...

fm3

## Detailed Description - Affected library: webknossos To interoperate with other libraries with additional functionality, we might want to add direct support for those. Especially navis seems to provide large...

jstriebel

Poll PIDs of child processes to detect OOM killing

4

When using multiprocessing (via clustertools), it can happen that the child processes are killed due to OOM. If the OOM killer decides to kill the children, the parent potentially waits...

philippotto

- [ ] `for_each_chunk` paired with executors is a powerful primitive for many analysis. Add an example that shows how it can be used - [ ] Export a dataset...

jstriebel