Quentin Blampey
Quentin Blampey
- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [ ]...
Hello, The depreciated method `AnnData.concatenate` is used when running `batch_removal` (see [here](https://github.com/theislab/scgen/blob/master/scgen/_scgen.py#L268)). This only throws a warning with `anndata==0.9` and `pandas
Hello, Thanks again for the library. In another issue (#3), you mentioned filtering low-quality genes based on active learning. I'm already using some basic filters (based on counts and cell...
Hello @VPetukhov, Thanks again for Baysor, it is a really efficient tool. I have an issue in the rare case when I don't have enough transcript count per prior cell...
Hello, In the documentation [here](https://spatialdata.scverse.org/en/latest/generated/spatialdata.models.Image2DModel.html), `Image2DModel.parse` has a `chunks` argument. Contrary to what suggests the documentation, this argument is only used when creating a `MultiscaleSpatialImage` I was expecting that it...
The `snakemake` pipeline should be translated to `nextflow` to reach more users. Don't hesitate to comment this issue to show your interest, else we keep it as a low priority...
Hello, When plotting an image, it seems that there is a 0.5-pixel shift. This is not visible for large images but becomes very visible if we zoom in, and, mostly,...
Hello, When rendering shapes, I get an error when trying to color shapes by a column of dtype `object` (containing strings) instead of dtype `category`. It would be great to...
Adding stitching to the CosMX reader. It's also possible to load one FOV only (if desired), and reading the proteins has also been added. This is still a very early...
Writing MERSCOPE data may use a lot of RAM. This is because the `.tif` image chunks are not detected when using `imread` from `dask_image`, so the full image has to...