scverse/spatialdata

Issues

• idea: point on-disk representation using OME-NGFF

  #789 opened a month ago by keller-mark
  2

• How to open the current Zarr based image data as OME-Zarr

  #805 opened 17 days ago by tischi
  0

• Why is it necessary to produce invalid OME-Zarr images?

  #803 opened 19 days ago by tischi
  3

• Brainstorm spatialdataDB

  #775 opened 17 days ago by lopollar
  2

• Elements should be validated before starting to write

  #804 opened 17 days ago by timtreis
  0

• Update documentation on how to make a release

  #802 opened 20 days ago by grst
  0

• Integration Testing CI Test Failure on python 3.10

  #801 opened 22 days ago by scverse-bot
  0

• Integration Testing CI Test Failure on python 3.12

  #800 opened 22 days ago by scverse-bot
  0

• Option to output GeoArrow-encoded parquet from geopandas

  #799 opened 23 days ago by keller-mark
  0

• class not supported when parsing a multipolygon with ShapesModel.parse

  #797 opened a month ago by mezwick
  1

• Choosing a performance profiling framework

  #769 opened a month ago by berombau
  1

• Harmonize artifical dataset creation

  #796 opened a month ago by berombau
  1

• Developer documentation on how to profile for performance

  #764 opened a month ago by berombau
  3

• Error loading sample 10X Xenium dataset

  #730 opened 2 months ago by alexmascension
  4

• Rename SpatialElements

  #793 opened a month ago by Marius1311
  0

• Importing Mass Spec Imaging Data into SpatialData

  #737 opened 2 months ago by blakesells7
  5

• Improving ergonomics for channel names handling

  #750 opened a month ago by LucaMarconato
  2

• Minor ergonomics/usability improvements

  #770 opened 2 months ago by quentinblampey
  2

• `rasterize` converts labels to images

  #783 opened a month ago by aeisenbarth
  0

• User documentation on how to setup jobs or run large analysis

  #768 opened 2 months ago by berombau
  1

• User notebook showcasing SpatialData speed

  #762 opened 2 months ago by berombau
  1

• Add a glossary in the docs

  #782 opened a month ago by quentinblampey
  0

• New docs section: how to integrate `spatialdata` in your tool

  #751 opened 2 months ago by LucaMarconato
  1

• Convenient function to read shapes and add them to the SpatialData object

  #772 opened a month ago by quentinblampey
  1

• Annotating coordinate systems

  #780 opened a month ago by LucaMarconato
  1

• Dask dataframe vs Polars

  #731 opened a month ago by gouinK
  2

• Cannot write sdata with tables to external SSD

  #776 opened a month ago by josenimo
  2

• New easier table notebook

  #749 opened 2 months ago by LucaMarconato
  1

• New easier intro notebooks

  #748 opened 2 months ago by LucaMarconato
  1

• Recommending a workflow for tiling (deep learning use case)

  #774 opened a month ago by berombau
  0

• reticulate spatialdata-io for readers & writing SpatialData .zarr

  #773 opened a month ago by HelenaLC
  0

• Benchmark spatial partitioning in dask geopandas

  #739 opened 2 months ago by LucaMarconato
  1

• Trouble installing with uv on python 3.10 and above

  #740 opened a month ago by keller-mark
  0

• Unable import SpatialData with the latest version of Xarray

  #735 opened a month ago by srivarra
  1

• Benchmarks performance on HPC

  #741 opened 2 months ago by LucaMarconato
  1

• Technology focus: Xenium is missing from read the docs.io

  #766 opened 2 months ago by OnkarMulay
  0

• User documentation on different methods of benchmarking with SpatialData

  #763 opened 2 months ago by berombau
  0

• Faster version `aggregate()` method available

  #744 opened 2 months ago by LucaMarconato
  2

• Parallelize `aggregate()`

  #743 opened 2 months ago by LucaMarconato
  1

• Having auto-completion when using spatialdata-plot

  #755 opened 2 months ago by quentinblampey
  0

• Access spatialdata-io from spatialdata

  #754 opened 2 months ago by quentinblampey
  0

• Organizing the docs API into sections

  #753 opened 2 months ago by quentinblampey
  0

• Make a biological transformation notebook

  #747 opened 2 months ago by LucaMarconato
  1

• CLI for `get_data_extent()` and `bounding_box_query()`

  #746 opened 2 months ago by LucaMarconato
  0

• CLI for modular creation/edit/concatenation of `SpatialData` objects

  #745 opened 2 months ago by LucaMarconato
  0

• Benchmark geopandas query methods

  #742 opened 2 months ago by LucaMarconato
  1

• Any way to map the probes sequences with the bins?

  #738 opened 2 months ago by Rafael-Silva-Oliveira
  0

• Transformation inconsistency between on-disk and in-memory usage

  #736 opened 2 months ago by quentinblampey
  0

• Detach SpatialData object from its Zarr store

  #733 opened 2 months ago by Marius1311
  3

• 'SpatialData' object has no attribute 'pl'

  #727 opened 3 months ago by chrismahony
  1