scverse/spatialdata

Issues

• Naming constraints break compatibility with existing datasets

  #624 opened 2 months ago by aeisenbarth
  7

• Errors on plotting features in the anndata of my spatialdata object

  #667 opened a month ago by joonlee3
  2

• Bounding box query vs polygon query for circles

  #669 opened a month ago by LucaMarconato
  1

• Plotting cropped Spatialdata leads to polygons protruding the viewport

  #644 opened a month ago by pakiessling
  3

• No matching definition for argument type

  #666 opened a month ago by wangjiawen2013
  1

• Error on the tutorial Deep learning example on image tiles

  #652 opened a month ago by aalia09123
  6

• legend height

  #665 opened a month ago by wangjiawen2013
  0

• index is out of bounds

  #663 opened a month ago by wangjiawen2013
  1

• Disallow zero-len dataframes when parsing

  #662 opened a month ago by LucaMarconato
  0

• Problem with substituting sdata.table with external AnnData

  #659 opened a month ago by gboscagli
  3

• Fail gracefully when circles have invalid radius

  #655 opened a month ago by LucaMarconato
  3

• Import Error: cannot import name '_get_unique_label_values_as_index'

  #641 opened a month ago by autumnfe
  1

• Better handing of data with non monotonically increasing index in `PointsModel.parse()`

  #649 opened a month ago by LucaMarconato
  0

• `rasterize_bins()` problem with coordinate transformations and with polygons.

  #650 opened a month ago by LucaMarconato
  2

• simplify tests where `Identity()` was needed as last transformation in a sequence

  #645 opened a month ago by LucaMarconato
  1

• `ImageTilesDataset` not in docs

  #642 opened a month ago by LucaMarconato
  0

• Faster implementation available for `vectorize()`

  #634 opened 2 months ago by LucaMarconato
  3

• Missing filtered table in polygon_query() of MERFISH data

  #633 opened 2 months ago by simonmfr
  4

• ImageTilesDataset throws RuntimeError during validation when instantiated

  #628 opened 2 months ago by tsvvas
  5

• TypeError: expected str, bytes or os.PathLike object, not list

  #637 opened 2 months ago by gboscagli
  2

• check on `c_coords` should be one the output data in `map_raster`

  #597 opened 2 months ago by giovp
  20

• concatenate tables or not

  #635 opened 2 months ago by wangjiawen2013
  1

• Improvement to the docs

  #631 opened 2 months ago by LucaMarconato
  1

• Invalid shapes during vectorization

  #583 opened 3 months ago by quentinblampey
  0

• Installation error in Intel processor Macbook

  #632 opened 2 months ago by shashkat
  3

• Workaround to use aggregate on elements of different shapes?

  #618 opened 2 months ago by tsvvas
  6

• Drop `region` (`region_key` and `instance_key` are enough)

  #629 opened 2 months ago by LucaMarconato
  0

• `get_element_instances` and `get_centroids` should not (?) return zero element

  #614 opened 2 months ago by giovp
  5

• Aggregation notebook is missing output

  #612 opened 2 months ago by ivirshup
  1

• Potential api change transform_element_to_coordinate_system

  #604 opened 2 months ago by melonora
  1

• multiprocessing for dataloader

  #590 opened 3 months ago by xiao233333
  2

• NotImplementedError when converting shape to label

  #609 opened 2 months ago by wangjiawen2013
  2

• `set_table_annotates_spatialelement` doesn't return a valid table

  #580 opened 2 months ago by giovp
  5

• Can't save transformation result

  #558 opened 2 months ago by Ithinky
  6

• Saving large files to .zarr

  #571 opened 2 months ago by asom
  3

• set_table_annotates_spatialelement error

  #603 opened 2 months ago by wangjiawen2013
  11

• numpy 2.0.0 support

  #602 opened 2 months ago by LucaMarconato
  0

• Issue with aggregation when `.attrs` is replaced instead of `.attrs['transform']`

  #600 opened 2 months ago by LucaMarconato
  0

• MultiScaleImage datatree.DataTree attrs in sdata object lost when writing to disk

  #576 opened 3 months ago by simone-codeluppi
  8

• `_get_element_annotators()` should be public.

  #595 opened 2 months ago by LucaMarconato
  1

• Behavior when the landmarks for alignment are chosen without respecting the order

  #586 opened 3 months ago by LucaMarconato
  0

• Experiment with rasterization on Visium HD like

  #572 opened 3 months ago by LucaMarconato
  1

• sdata does not save when chunks are not equal

  #581 opened 3 months ago by lotte-vandevreken
  0

• Optimize writing performance for `MultiscaleSpatialImage`

  #577 opened 3 months ago by LucaMarconato
  1

• Registering a new table with a coordinate system

  #573 opened 3 months ago by pakiessling
  1

• How to create a spatialdata object from a VisiumHD dataset preprocessed by spaceranger?

  #563 opened 3 months ago by OMIC-coding
  8

• Querying points doesn't filter the associated table

  #567 opened 3 months ago by LucaMarconato
  1

• `polygon_query()` with `filter_table=True` on labels should filter the table.

  #564 opened 3 months ago by LucaMarconato
  0

• Test aggregation of vector data by vector data when `agg_func` is a `list` of `str`

  #561 opened 4 months ago by LucaMarconato
  0

• bug: BaseTransformation has no .copy() method, but `parse` tries to use it

  #559 opened 4 months ago by VolkerH
  1