Seurat V5 on MERFISH data

[YidaZhang0628]

I am planning to use Seurat V5 on a MERFISH dataset. The tutorial uses LoadVizgen function to read the files. However, I don't have hdf5r files from segmentation. Therefore, I won't be able to use LoadVizgen. I can read the data using ReadVizgen but it results in a plain list instead of a Seurat object. Any idea on how to read MERFISH data without segmentation information into a Seurat object?

[resc0034]

I have the same question. It seems output from Vizgen MERSCOPE experiments will no longer provide a cell_boundaries folder with .hdf5 files. Instead, the output will include a "cell_boundaries.parquet" file. Are there any plans to update the LoadVizgen() function for use with a parquet file?

[alikhuseynov]

It seems that you have Cellpose output. I submitted a PR handle Cellpose output #7190
See also this #7080
You may it devtools::install_github(repo = "alikhuseynov/seurat", ref = "feat/vizgen")
To load Vizgen this workflow could help make Seurat objects

[MaycieS]

Hello. I am having issues using LoadVizgen() and ReadVizgen() with my MERFISH dataset still. I know there was a PR made for this, but I am still confused on how to fix the parquet issue. When I use the code below,

vizgen.obj <- ReadVizgen(data.dir = "E:\111124_MS_MB_Merfishy", transcripts = "E:\111124_MS_MB_Merfishy\cell_by_gene.csv", spatial = "E:\111124_MS_MB_Merfishy\cell_metadata.csv", molecules = "E:\111124_MS_MB_Merfishy\detected_transcripts.csv", type = "segmentations", mol.type = "microns", z=3L)

I get the error "Warning in ReadVizgen(data.dir = data_dir, transcripts = transcripts_path, :
180046 cells missing polygon information"

There were 50 or more warnings (use warnings() to see the first 50)". I am assuming that is because there is no hfad file anymore (replaced by parquet). What code am I supposed to run instead?

[alikhuseynov]

Hi. try to install this PR for Seurat5 devtools::install_github(repo = "alikhuseynov/seurat", ref = "vizgen_seurat5")
try to use this loading script

vizgen.obj <- ReadVizgen(data.dir = "E:\111124_MS_MB_Merfishy", transcripts = "E:\111124_MS_MB_Merfishy\cell_by_gene.csv", spatial = "E:\111124_MS_MB_Merfishy\cell_metadata.csv", molecules = "E:\111124_MS_MB_Merfishy\detected_transcripts.csv", type = "segmentations", mol.type = "microns", z=3L)

ReadVizgen doesn't make the object, it reads the data in a list, LoadVizgen needs to be used. Make sure that parquet file is somewhere/within your E:\111124_MS_MB_Merfishy directory.
hope this helps.

[MaycieS]

Thank you! That appeared to work, however I now cannot run the vizgen.obj <- SCTransform(vizgen.obj, assay = "Vizgen") function due to the class = list. I know I need this to be a Seurat Object in matrix form. Is there a way to fix that? Thanks, Maycie Maycie Schultz Sun Lab Biomedical Sciences Graduate Student University of Wyoming, Biological Sciences 1000 E University Ave, Laramie, WY 82071

…

________________________________ From: Alik Huseynov ***@***.***> Sent: 14 November 2024 02:55 To: satijalab/seurat ***@***.***> Cc: Maycie Schultz ***@***.***>; Comment ***@***.***> Subject: Re: [satijalab/seurat] Seurat V5 on MERFISH data (Discussion #7170) ◆ This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources. Hi. try to install this PR for Seurat5 devtools::install_github(repo = "alikhuseynov/seurat", ref = "vizgen_seurat5") try to use this loading script<https://github.com/alikhuseynov/add-on_R/blob/develop/R/example_read_load_vizgen_v2.R> vizgen.obj <- ReadVizgen(data.dir = "E:\111124_MS_MB_Merfishy", transcripts = "E:\111124_MS_MB_Merfishy\cell_by_gene.csv", spatial = "E:\111124_MS_MB_Merfishy\cell_metadata.csv", molecules = "E:\111124_MS_MB_Merfishy\detected_transcripts.csv", type = "segmentations", mol.type = "microns", z=3L) ReadVizgen doesn't make the object, it reads the data in a list, LoadVizgen needs to be used. Make sure that parquet file is somewhere/within your E:\111124_MS_MB_Merfishy directory. hope this helps. — Reply to this email directly, view it on GitHub<#7170 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFH4BBAK3KBNAXP62H5TH7D2ARXSDAVCNFSM6AAAAABRXNTKJ6VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTCMRVGIZDKNA>. You are receiving this because you commented.Message ID: ***@***.***>

[alikhuseynov]

ok, no worries.
You need vizgen.obj to be a Seurat object not an output list class after ReadVizgen. LoadVizgen returns Seurat object and that should work with SCTransform.