Marco

I would like to extend the compatibility with Python 3.11, torch 2.1, and pytorch-lightning 2.1.3. One fix was easy to make (e.g. change training_epoch_end into `on_training_epoch_end`). Another fix was about...

Shape's outline color from a table column

3

Currently, the color of a set of shapes can be set according to a column in the table, but for the outline, it's only possible to specify a single color...

Reduce reader memory consumption

2

It adds a new `output_path` parameter in a reader's function that allows to save every element of the spatialdata object as soon as it's created. This frees up part of...

Missing tiles in Xenium H&E image

4

I ran `xenium()` with default parameters on official data from 10x Genomics (such as https://www.10xgenomics.com/datasets/ffpe-human-breast-with-custom-add-on-panel-1-standard). However, I noticed that when I plotted the H&E image using the `spatialdata-plot` package, there...

Reduce readers' memory consumption

1

In the current implementation, a reader loads all the object from the raw files in memory and creates a `spatialdata` object. Is then the user's responsibility to save the object...

Change CellCharter name and default values

1

Thank you very much for implementing CellCharter! As I discussed in the past, @LLehner had to implement a simplified version of CellCharter to avoid adding new dependences. The most important...

Change niche flavor to cellcharter_simple and default distance = 3

1

## Description - Change `flavor` option in `calculate_niche to `cellcharter_simple` for CellCharter - Default `distance = 3` for `cellcharter_simple`. ## How has this been tested? `pytest` runs successfully. However, I...

Load Xenium mask labels using Dask

1

Towards #228 Replace the code to load the Xenium segmentation masks to use Dask to greatly reduce the memory consumption of the Xenium reader. I abandoned the idea of saving...