Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

CosMx FOVs being skipped #894

Open
jamesboot opened this issue Oct 2, 2024 · 1 comment
Open

CosMx FOVs being skipped #894

jamesboot opened this issue Oct 2, 2024 · 1 comment
Assignees
@michalk8

Comments

@jamesboot
Copy link

jamesboot commented Oct 2, 2024 •
edited
Loading

Description

When loading CosMx data from FOVs are skipped because they "do not exist in CellComposite folder" or "do not exist in CellLabels folder", however the FOVs do exist in these folders... Not sure what the issue is here, why these FOVs are being skipped or how to fix, any help would be great!

...

Minimal reproducible example

adata2 = sq.read.nanostring(
    path=sample_dir,
    counts_file=counts_file,
    meta_file=meta_file,
    fov_file=fov_file
)

Traceback

WARNING: FOV `197` does not exist in CellComposite folder, skipping it.
WARNING: FOV `570` does not exist in CellComposite folder, skipping it.
WARNING: FOV `558` does not exist in CellComposite folder, skipping it.
WARNING: FOV `646` does not exist in CellComposite folder, skipping it.
WARNING: FOV `642` does not exist in CellComposite folder, skipping it.
WARNING: FOV `271` does not exist in CellComposite folder, skipping it.
WARNING: FOV `176` does not exist in CellComposite folder, skipping it.
WARNING: FOV `614` does not exist in CellComposite folder, skipping it.
WARNING: FOV `272` does not exist in CellComposite folder, skipping it.
WARNING: FOV `496` does not exist in CellComposite folder, skipping it.
WARNING: FOV `267` does not exist in CellComposite folder, skipping it.
WARNING: FOV `297` does not exist in CellComposite folder, skipping it.
WARNING: FOV `568` does not exist in CellComposite folder, skipping it.
WARNING: FOV `447` does not exist in CellComposite folder, skipping it.
WARNING: FOV `367` does not exist in CellComposite folder, skipping it.
WARNING: FOV `98` does not exist in CellComposite folder, skipping it.
WARNING: FOV `421` does not exist in CellComposite folder, skipping it.
WARNING: FOV `564` does not exist in CellComposite folder, skipping it.
WARNING: FOV `563` does not exist in CellComposite folder, skipping it.
WARNING: FOV `559` does not exist in CellComposite folder, skipping it.
WARNING: FOV `517` does not exist in CellComposite folder, skipping it.
WARNING: FOV `222` does not exist in CellComposite folder, skipping it.
WARNING: FOV `707` does not exist in CellComposite folder, skipping it.
WARNING: FOV `683` does not exist in CellComposite folder, skipping it.
WARNING: FOV `292` does not exist in CellComposite folder, skipping it.
WARNING: FOV `192` does not exist in CellComposite folder, skipping it.
WARNING: FOV `739` does not exist in CellComposite folder, skipping it.
WARNING: FOV `562` does not exist in CellComposite folder, skipping it.
WARNING: FOV `607` does not exist in CellComposite folder, skipping it.
WARNING: FOV `247` does not exist in CellComposite folder, skipping it.
WARNING: FOV `743` does not exist in CellComposite folder, skipping it.
WARNING: FOV `491` does not exist in CellComposite folder, skipping it.
WARNING: FOV `607` does not exist in CellLabels folder, skipping it.
WARNING: FOV `568` does not exist in CellLabels folder, skipping it.
WARNING: FOV `222` does not exist in CellLabels folder, skipping it.
WARNING: FOV `564` does not exist in CellLabels folder, skipping it.
WARNING: FOV `562` does not exist in CellLabels folder, skipping it.
WARNING: FOV `98` does not exist in CellLabels folder, skipping it.
WARNING: FOV `496` does not exist in CellLabels folder, skipping it.
WARNING: FOV `367` does not exist in CellLabels folder, skipping it.
WARNING: FOV `558` does not exist in CellLabels folder, skipping it.
WARNING: FOV `421` does not exist in CellLabels folder, skipping it.
WARNING: FOV `646` does not exist in CellLabels folder, skipping it.
WARNING: FOV `272` does not exist in CellLabels folder, skipping it.
WARNING: FOV `642` does not exist in CellLabels folder, skipping it.
WARNING: FOV `614` does not exist in CellLabels folder, skipping it.
WARNING: FOV `297` does not exist in CellLabels folder, skipping it.
WARNING: FOV `197` does not exist in CellLabels folder, skipping it.
WARNING: FOV `271` does not exist in CellLabels folder, skipping it.
WARNING: FOV `739` does not exist in CellLabels folder, skipping it.
WARNING: FOV `491` does not exist in CellLabels folder, skipping it.
WARNING: FOV `743` does not exist in CellLabels folder, skipping it.
WARNING: FOV `192` does not exist in CellLabels folder, skipping it.
WARNING: FOV `292` does not exist in CellLabels folder, skipping it.
WARNING: FOV `176` does not exist in CellLabels folder, skipping it.
WARNING: FOV `570` does not exist in CellLabels folder, skipping it.
WARNING: FOV `267` does not exist in CellLabels folder, skipping it.
WARNING: FOV `563` does not exist in CellLabels folder, skipping it.
WARNING: FOV `707` does not exist in CellLabels folder, skipping it.
WARNING: FOV `447` does not exist in CellLabels folder, skipping it.
WARNING: FOV `247` does not exist in CellLabels folder, skipping it.
WARNING: FOV `559` does not exist in CellLabels folder, skipping it.
WARNING: FOV `683` does not exist in CellLabels folder, skipping it.
WARNING: FOV `517` does not exist in CellLabels folder, skipping it.
WARNING: FOV `98` does not exist, skipping it.
WARNING: FOV `176` does not exist, skipping it.
WARNING: FOV `192` does not exist, skipping it.
WARNING: FOV `197` does not exist, skipping it.
WARNING: FOV `222` does not exist, skipping it.
WARNING: FOV `247` does not exist, skipping it.
WARNING: FOV `267` does not exist, skipping it.
WARNING: FOV `271` does not exist, skipping it.
WARNING: FOV `272` does not exist, skipping it.
WARNING: FOV `292` does not exist, skipping it.
WARNING: FOV `297` does not exist, skipping it.
WARNING: FOV `367` does not exist, skipping it.
WARNING: FOV `421` does not exist, skipping it.
WARNING: FOV `447` does not exist, skipping it.
WARNING: FOV `491` does not exist, skipping it.
WARNING: FOV `496` does not exist, skipping it.
WARNING: FOV `517` does not exist, skipping it.
WARNING: FOV `558` does not exist, skipping it.
WARNING: FOV `559` does not exist, skipping it.
WARNING: FOV `562` does not exist, skipping it.
WARNING: FOV `563` does not exist, skipping it.
WARNING: FOV `564` does not exist, skipping it.
WARNING: FOV `568` does not exist, skipping it.
WARNING: FOV `570` does not exist, skipping it.
WARNING: FOV `607` does not exist, skipping it.
WARNING: FOV `614` does not exist, skipping it.
WARNING: FOV `642` does not exist, skipping it.
WARNING: FOV `646` does not exist, skipping it.
WARNING: FOV `683` does not exist, skipping it.
WARNING: FOV `707` does not exist, skipping it.
WARNING: FOV `739` does not exist, skipping it.
WARNING: FOV `743` does not exist, skipping it.
AnnData object with n_obs × n_vars = 521946 × 1165
    obs: 'fov', 'Area', 'AspectRatio', 'Width', 'Height', 'Mean.PanCK', 'Max.PanCK', 'Mean.CD68', 'Max.CD68', 'Mean.Membrane', 'Max.Membrane', 'Mean.CD45', 'Max.CD45', 'Mean.DAPI', 'Max.DAPI', 'cell_id', 'assay_type', 'version', 'Run_Tissue_name', 'Panel', 'slide_ID', 'unassignedTranscripts', 'nCount_RNA', 'nFeature_RNA', 'nCount_negprobes', 'nFeature_negprobes', 'nCount_falsecode', 'nFeature_falsecode', 'Area.um2', 'CenterX_global_px', 'CenterY_global_px', 'cell', 'cell_ID'
    uns: 'spatial'
    obsm: 'spatial', 'spatial_fov'

Versions

scanpy==1.10.3 anndata==0.10.9 umap==0.5.6 numpy==1.26.4 scipy==1.14.1 pandas==2.2.3 scikit-learn==1.5.2 statsmodels==0.14.3 igraph==0.11.6 pynndescent==0.5.13 squidpy==1.6.1

...
@jamesboot
Copy link
Author

jamesboot commented Nov 5, 2024 •
edited
Loading

UPDATE

Attempted to load the data using spatialdata-io function cosmx() and had some errors, turned out to be due to empty FOVs in the dataset. From what I can tell these were the same FOVs being skipped above.

Linking the issue here: scverse/spatialdata-io#213

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@michalk8 michalk8

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@jamesboot @michalk8