Jose Nimo
Jose Nimo
Dear @quentinblampey I am in the process of changing the provided Snakefile to run many samples (images) at once. I am replacing the inputs and outputs paths to include the...
**Recommendation: attach a minimal working example** Generally, the easier it is for us to reproduce the issue, the faster we can work on it. It is not required, but if...
**Describe the bug** I am writing large sdata objects to zarr, and the Kernel fails in an unpredictable manner. I parse the image into sdata, a large mIF image (15,...
Dear spatialdata devs, I just switched to pixi, and really like it. However I am running with some issues specifically with `spatialdata`. I don't want to enforce this as a...
Dear @ajitjohnson, I am trying to phenotype some immune cells that are very close to each other. In the figure below, you can see that the cells with yellow points...
## Description running snakemake locally defaults to looking for a conda environment called `sopa` ## Reproducing the issue create sopa + snakemake env with `uv` and then run snakemake locally...
Dear devs, Would multiview-stitcher be able to stitch and register multiplex immunofluorescence datasets? I work with datasets created by MACSima, CyCIF, and other similar methods. I am currently using [ashlar](https://github.com/labsyspharm/ashlar),...