Benjamin Rombaut
Benjamin Rombaut
By supporting FSStore as input, more complex ZarrLocations are possible like private remote stores.
When evaluating (e.g. at `https://dodona.be/nl/feedbacks/FEEDBACK_ID/`), I want to look at the student's solution in other lists, which use the SUBMISSION_ID. Having the SUBMISSION_ID somewhere so I can copy-paste it would...
Closes #441, depends on (https://github.com/ome/ome-zarr-py/pull/349)
Right now, there is support for local .zarr stores and remote stores publically accessible via HTTP or S3. Private remote stores are more difficult, as they need certain options or...
This works: ```python import zarr import spatialdata as sd root = zarr.open( "s3://bucket_name/spatial-sandbox/visium_associated_xenium_io.zarr", storage_options={ "endpoint_url": "https://objectstor.vib.be", }, ) sdata = sd.SpatialData.read(root) # sdata has content ``` This does not work:...
This is a tracking issue for some of the current issues when having a SpatialImage of circa >10 channels in SpatialData: - [ ] **Vizarr, Avivator, Vitessce fail when loading...
The napari CLI has support for loading one or more plugins. Supporting this fully is beneficial as this is what new users with napari experience will expect. When combining CLI...
Filtering does not work if an extra table is present not related to an element (which is a use case to save analysis results). ```python # napari_spatialdata/utils/_utils.py:361 for element_type, element_name,...
This tries to solve #155. Lung_adc_demo ```python from spatialdata_io import macsima sdata = macsima('./Lung_adc_demo', subset=1000) sdata ``` ``` SpatialData object with: └── Images └── 'Lung_adc_demo': MultiscaleSpatialImage[cyx] (116, 1000, 1000), (116,...
A reader to support reading data from the Miltenyi MACSima platform. It should support the published datasets: - [ ] [Liver Cell Atlas](https://livercellatlas.org/download.php) (old data stitched and already processed) -...