ArneD

Problems reproducing results on "I2B2 2006: Smoker Identification" dataset

5

First of all, thanks for the interesting paper and code. However, I am having problems reproducing the results reported in the paper. I tried reproducing the results reported on the...

automatic backing of sdata.tables

2

I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail...

PR for illustration of possible workflow for adding elements to spatialdata object inspired by https://github.com/scverse/spatialdata/blob/582622f689a7e05421e9d066f98baf702549978f/tests/io/test_readwrite.py#L136 and related to discussion https://github.com/scverse/spatialdata/discussions/520. Currently only implemented for image and labels, but similar approaches...

Apply function

1

Implementation of an apply function for image layers in spatialdata object. Basic usage is similar to squidpy’s apply function, E.g.: ``` def _multiply(image, parameter=2): return image * parameter fn_kwargs =...

Adding image to same slot for backed sdata

1

When writing an image to zarr with overwrite=True, I found some unexpected behaviour. Below I give a mimimal example to reproduce the issue. This works, as expected. I can overwrite...

relabel block

5

Follow up PR for https://github.com/scverse/spatialdata/pull/588, see discussion https://github.com/scverse/spatialdata/issues/597 for relabeling in case output data is a labels layer (i.e. `dims` does not contain `c`) via use of a bit shift.

spatialdata aggregate 3D support + relatively slow on large images

2

**Is your feature request related to a problem? Please describe.** - `spatialdata.aggregate` does not support 3D, - `spatialdata.aggregate` can be slow on large images. - `spatialdata.aggregate` does not allow aggregation...

Visium hd

6

This adds support for annotating the resulting tables with corresponding labels layers (the bins). Annotating the table by a labels layer has the advantage that the bins, and their expression...

Thanks for the great package! I want to visualize a spatialdata object using vitessce using the widget. I used the code from https://github.com/vitessce/vitessce-python/blob/main/docs/notebooks/spatial_data_blobs.ipynb. This notebook works, but now I also...

Feature request, write_element does not materialize computation in in-memory SpatialData Object

7

When using `sdata.write_element()`, the Dask computation remains lazy in the in-memory SpatialData object, when SpatialData object is backed by disk. So each time we do `sdata.write_element(...)`, we need to call...