webknossos-libs

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## Detailed Description Affected library: webknossos Currently, `ds.add_layer_from_images()` and `Dataset.from_images()` can use the pims bioformats reader when `use_bioformats` is explicitly set to true. It would be great to use the...

jstriebel

Document command line parameters

2

From a quick look, not all command line parameters are documented, some of them fairly important, for example `--max` to specify the maximum down-sampled resolution, or the different interpolation modes....

daniel-wer

Auto-detect segmentation layers

2

When cubing datasets the user has to specify which layers are segmentation layers. It would be helpful to add a heuristic that auto-determines this. E.g. find patches of uniform color/id...

fm3

Restructure wkcuber commands / Build new CLI

1

The commands in `wkcuber` have grown over time. I think it would be time to clean that up a bit. I think we should use sub commands instead of individual...

normanrz

[client] Use single httpx client for requests & parallelize them

4

Currently, the generated client uses a fresh httpx client for every request (see also issue https://github.com/openapi-generators/openapi-python-client/issues/202 about this), and the resumable-client currently also for one session (but accepts a client...

jstriebel

## Detailed Description - Affected library: webknossos Call webKnossos and its datastores to refresh the dataset list. Maybe `wk.Dataset.trigger_check_for_datasets()`. ## Use Cases & Context I create a new dataset and...

normanrz

## Detailed Description Affected library: webknossos Atm, annotations always contain local metadata and a local skeleton. The volume annotations might be locally available, but not necessarily, and can be streamed...

jstriebel

Some users uploaded image data in hdf5 format. A converter should be added. If I interpret the discussion at https://github.com/scalableminds/webknossos-libs/issues/748 correctly, the bioformats lib already supports this, but pims does...

fm3

Some users have uploaded datasets as video files, e.g. avi. There should be a converter for its frames.

fm3

Affected library: `webknossos` ## Use Cases & Context In https://github.com/scalableminds/webknossos/pull/6414 we introduce the (optional) largest segment id to the NML format. We should be able to read and save them...

jstriebel