scverse/spatialdata-notebooks

Issues

• Update Xenium dataset

  #110 opened 5 months ago by LucaMarconato
  0

• Check reproducibility of Steinbock and NanoString notebooks on Windows

  #106 opened 5 months ago by LucaMarconato
  0

• Update the table with data with info from the paper

  #18 opened 9 months ago by LucaMarconato
  1

• Feedback: new notebook on how to convert your data to Zarr/SpatialData

  #21 opened 9 months ago by LucaMarconato
  1

• Notebook on region, region_key, instance_key

  #22 opened 9 months ago by LucaMarconato
  1

• The tutorial samples did not work for me

  #31 opened 9 months ago by cshuxteau
  5

• Broken data for deep learning example on image tiles

  #44 opened 9 months ago by npeschke
  2

• Query notebook expects Visium data different from the one in S3

  #54 opened 9 months ago by LucaMarconato
  1

• NotImplementedError: Multiscale images are not implemented yet

  #70 opened 9 months ago by duongvtt96
  2

• Typo in MERFISH tutorial

  #77 opened 10 months ago by WeilerP
  0

• Notebook to illustrate what speed-ups we automatically do in the background.

  #59 opened a year ago by timtreis
  0

• mcmicro_io.zip cell and nucleus bitmasks are the same

  #52 opened a year ago by keller-mark
  4

• Multiple spatialdata objects in napari not supported

  #38 opened a year ago by melonora
  1

• `spatial_query` tutorial breaks at first plot

  #41 opened a year ago by MobiTobi
  2

• Replace `os.path` with `Path` and "unzip" with `shutil.unpack_archive`

  #40 opened a year ago by LucaMarconato
  1

• Image not in visium data

  #37 opened a year ago by melonora
  3

• Nested sandbox.zarr in 00_xenium_and_visium.ipynb

  #36 opened a year ago by melonora
  8

• Refactor Xenium + Visium paths and use better names

  #39 opened a year ago by LucaMarconato
  1

• Notebook on 3D data and on images from multiple imaging cycles

  #23 opened 2 years ago by LucaMarconato
  0

• Removing the docs?

  #10 opened 2 years ago by LucaMarconato
  1

• install instructions

  #4 opened 2 years ago by will-moore
  2