Marius Lange

Ordering of the timepoints

2

In my AnnData object, I have a field `adata.obs['day']`, which is categorical, calling `adata.obs['day'].cat.categories` yields ``` Index(['0', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '15',...

Meaning and function of the `n_components` parameter

1

Harmony has a `n_components` parameter, which, according to the docstring: ```:param pc_components: Minimum number of principal components to use. Specify `None` to use pre-computed components``` That value is used for...

Hi Cassiopeia team, I was wondering whether there would be a place in the documentation where I can find more information about the computation of tree likelihoods in Cassiopeia? For...

`.impute` consumes too much memory

5

I'm trying to call `problem.impute()` on a solved (linear) spatial mapping problem of dimensions `n_source=17806` (spatial data) by `n_target=13298` (single-cell data) for `n_genes=2039`. This is just a full-rank Sinkhorn problem...

LineageProblem error

3

Hi there, I'm getting `ValueError: Unable to solve a quadratic problem with `alpha = 1` and `xy` supplied.` when trying to solve a `LineageProblem` with `alpha=1.0` and `joint_attr=None`.

Pull or push `.obsm` or `.varm` annotations.

2

Thank you for this amazing package! **Is your feature request related to a problem? Please describe.** Currently, there does not seem to be a build-in method to pull or push...

Bug in the MERFISH Technology tutorial

1

**Describe the bug** Hi there, I'm running the public MERFISH tutorial using spatialdata `0.2.2` and spatialdata_plot `0.2.4` (https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/technology_merfish.html) and when I execute the final cell containing ```Python import matplotlib.pyplot as...

Is there currently a way to plot 3D data?

2

I'm looking for even just the simplest case, i.e. fixing a z-location and visualizing x, y coordinates in 2D. I tried naively with spatialdata-plot, i.e. just `sdata.pl.render_images("image", channel="DAPI").pl.show()`, but that...

`sopa.segmentation.transcripts.resolve` for Baysor segmentation fails

4

Thanks for this amazing tool! ## Description I have an sdata object with more than one image (MERSCOPE data with 7 z slices), and I used Baysor trough the sopa...

Handling pseudo 3D information

2

**Is your feature request related to a problem? Please describe.** Cellpose natively supports 3D segmentation; we have so far used it in "pseudo 3D mode", where you segment each z-slice...