Vizgen again

[HSvitina]

Dear Seurat developers
I have my single-nuclei seq dataset processed in Seurat. I also have Vizgen MERSCOPE assay. I have problems reading/loading my Merfish. I see, it was discussed a lot, about parquet files etc - #7080

When I try to load files - I have this.

vizgen.obj <- LoadVizgen(data.dir = "D:/analysis_outputs_D7C/", + fov = "D7CfromR") Warning in ReadVizgen(data.dir = data.dir, filter = "^Blank-", type = c("centroids", : Cannot find cell boundary H5 files Error in UseMethod(generic = "CreateSegmentation", object = coords) : no applicable method for 'CreateSegmentation' applied to an object of class "NULL" --   | > >

If I try to follow new script https://github.com/alikhuseynov/add-on_R/blob/develop/R/example_read_load_vizgen_v2.R
It does not even try to read something
Error in LoadVizgen(data.dir = dir_use, fov = "merfish.test", assay = "Vizgen", :
unused arguments (metadata = c("volume", "fov"), type = c("segmentations", "centroids"), add.zIndex = TRUE, update.object = TRUE, use.BiocParallel = TRUE, workers.MulticoreParam = 14, min.area = 5, add.molecules = TRUE, verbose = TRUE)

My seurat package is new, ver 5. Can you suggest something, please?

[alikhuseynov]

Hi @HSvitina,
I'm not from Seurat dev team, and the PR I did is to support loading .parquet:

• Support to handle .parquet output from Vizgen #7190

..I try to follow new script https://github.com/alikhuseynov/add-on_R/blob/develop/R/example_read_load_vizgen_v2.R

That script works only on that PR.
These should work for version 4 or 5:

• This branch is for Seurat and SeuratObject v4 to install -> remotes::install_github(repo = 'alikhuseynov/seurat', ref = 'feat/vizgen')
• This one is for v5, to install -> remotes::install_github(repo = 'alikhuseynov/seurat', ref = 'vizgen_seurat5') try to use this one.

Also, HDF5 files are no longer the output from Vizgen, it's all in .parquet now. A potential solution for H5 is here

I mainly co-develop SpatialFeatureExperiment Bioc package
If you want you can use these:
loading Vizgen Merfish and analysis workflow

Hope this helps.
cheers

[zskylarli]

Closing due to inactivity, but thank you @alikhuseynov for offering a solution! We are actively working on merging PRs and also adapting Seurat to ensure compatibility with changes in data formats for our spatial pipelines. @HSvitina if further issues come up with our loaders, please don't hesitate to report them as new issues!