CosMx FOVs being skipped

[jamesboot]

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

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