Alik Huseynov

you have these versions `SeuratObject_5.0.1 Seurat_4.3.0.9002` - This branch is for Seurat and SeuratObject v4 `remotes::install_github(repo = 'alikhuseynov/seurat', ref = 'feat/vizgen')` - This one is for v5 `remotes::install_github(repo = 'alikhuseynov/seurat',...

> vizgen.obj[[Images(vizgen.obj)[1]]][["segmentation"]] > A spatial segmentation for 3323 cells ok, it does read some segmentations It seems to be an issue here -> https://github.com/alikhuseynov/seurat/blob/vizgen_seurat5/R/preprocessing.R#L3100-L3101 or here -> https://github.com/satijalab/seurat/blob/master/R/preprocessing.R#L2778-L2780 basically `sp$fov`...

`mols.qv.threshold` this arg only filters the molecule (transcript) coordinates not the count matrix. https://github.com/satijalab/seurat/blob/develop/R/preprocessing.R#L2215 The count matrix is already filtered by default (QC > 20) in Xenium pipeline. So your...

this similar issue #109 might help

@angie-john, did it finally work?

Thanks for the comment. Do you mean several public Vizgen datasets or in general Cellpose output data? `z = 3L` arg for z-plane is a default and was there before...

..just to confirm: Vizgen is using just one z-plane, ie middle plane of the tissue for Cellpose segmentation.

The last commit should fix most of the bugs, supports old and new Vizgen data outputs, and optimized parallelization If any bugs or something I missed, let me know please....

> This worked on all my test data and scenarios. > > The only other suggestion I would have is making `molecules` an optional input (since the file can be...

> Any updates for this pull request? ..sorry I was a bit busy, will be adding a new arg `add.molecules = TRUE` in `LoadVizgen()` to have `molecules` FOV optionally added...