Alik Huseynov
Alik Huseynov
Could you please show the whole error output and `traceback()` What does the `ReadAkoya()` outputs in this case?
I'm not from the dev team though, it's bit difficult to debug. What versions of `Seurat` and `SeuratObject` are you using? Does the `ReadAkoya()` work without an error? if yes,...
Probably it has something to do with your input file `230913_for_seurat.csv`. Did you specify `assay` variable, like `assay = "qupath.test"` or some relevant name? I never worked with QuPath, not...
`data$metada` with `0` cols seems weird. Also `data$matrix` looks strange, it should be a _sparse matrix with expression data_ I think this kind of coordinate for a single cell centroid...
what kind of spatial QCs would those be? I'm working a list of such QC (including image segmentation QCs, (geo) spatial metrics etc..) for implementation, if not already implemented in...
sounds good!
@dcjones could you please elaborate more on `poisfa` branch and what the it does (from the name I guess Poisson process)?
> Hi @alikhuseynov, sure thing. This branch tries to overcome the the issues the current version of Proseg has in high dimensionality settings by implementing probabilistic matrix factorization as part...
> Hi @alikhuseynov . Have you succeeded in installing from this branch? If so, could you share how you installed? Thanks! Hi @yihming, yes - on my Mac Monterey 12.4,...
@dcjones Thanks! Can one use nuclear stain image intensity (eg as hotspots) and/or of available the cell boundary stains to additionally support what `proseg` does? It looks like in the...