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Hello, My name is Vasily, I am a developer of the Immunarch package. Thank you for using it! Sorry for the late reply and thank you for providing the solution,...

Hi Fabio, My name is Vasily, I am one of the core team members maintaining immunarch. Currently, we are actively researching and implementing clonal lineage analysis of BCR receptors in...

Hello Antoine, Thank you for using immunarch. Could you please send a direct link for the Galson et al 2016 article? Best, Vasily

Hi @Pedro-Pei! Sadly no, I couldn't figure out how to use the package beyond CLI.

Thank you, Luca, this solution works for me. I was looking for it in the optimizations section in spatialdata tutorials, but it is confusing to go back and forth between...

Hi @timtreis, Thank you for checkin in on the issue. I managed to produce an image, but not without issues. First, the morphology_focus image after reading with `spatiadata_io.xenium()` has 5...

With `channel` I get the following error: ```python cropped.pl.render_images( "morphology_focus", palette=["#0F73E6", "#F300A5", "#A4A400", "#008A00"], channel=[0, 1, 2, 3], ).pl.show( title="Morphology image", coordinate_systems="global" ) ``` Error: ```python File [spatialdata_plot/pl/basic.py:862] 856 if...

A fully reproducible example: ```python ! curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_humanLung_Cancer_FFPE/Xenium_V1_humanLung_Cancer_FFPE_outs.zip --output-dir ../data ! mkdir ../data/Xenium_V1_humanLung_Cancer_FFPE_outs ! unzip ../data/Xenium_V1_humanLung_Cancer_FFPE_outs.zip -d ../data/Xenium_V1_humanLung_Cancer_FFPE_outs DATA_PATH = "../data/Xenium_V1_humanLung_Cancer_FFPE_outs" sdata = spio.xenium(DATA_PATH, n_jobs=-1) OUT_PATH = f"../output/{date.today()}" FILE_PATH...

Yes, this is how it looks like in the example above  What is the 5th channel here? Or should I ask this in the spatialdata_io issues?

Hi @timtreis, Seems like the 5th channel is empty: ```python >>> sdata.images["morphology_focus"]["scale0"]["image"].isel(c=4).sum(dim=["y", "x"]).values array(0, dtype=uint64) ```