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Updated Visium Spatial Gene Expression table row to Descendants of Visium Spatial Gene Expression
Added matrix requirements for Visium CytAssist Spatial Gene Expression, 11mm.
Design
Assay
"raw" required?
"raw" location
"normalized" required?
"normalized" location
Descendant of Visium Spatial Gene Expression
REQUIRED. Values MUST be de-duplicated molecule counts. All non-zero values MUST be positive integers stored as numpy.float32.
If uns['spatial']['is_single'] is False then each cell MUST contain at least one non-zero value.
If uns['spatial']['is_single'] is True then the unfiltered feature-barcode matrix (raw_feature_bc_matrix) MUST be used. See Space Ranger Feature-Barcode Matrices.
if assay_ontology_term_id is "EFO:0022860" for Visium CytAssist Spatial Gene Expression, 11mm, this matrix MUST contain 14336 rows; otherwise, this matrix MUST contain 4992 rows.
If the obs['in_tissue'] value is 1, then the cell MUST contain at least one non-zero value. If any obs['in_tissue'] values are 0, then at least one cell corresponding to a obs['in_tissue'] with a value of 0 MUST contain a non-zero value.
AnnData.raw.X unless no "normalized" is provided, then AnnData.X
STRONGLY RECOMMENDED
AnnData.X
The text was updated successfully, but these errors were encountered:
Changelog
X (Matrix Layers)
Design
numpy.float32
.If
uns['spatial']['is_single']
isFalse
then each cell MUST contain at least one non-zero value.If
uns['spatial']['is_single']
isTrue
then the unfiltered feature-barcode matrix (raw_feature_bc_matrix
) MUST be used. See Space Ranger Feature-Barcode Matrices.if
assay_ontology_term_id
is"EFO:0022860"
for Visium CytAssist Spatial Gene Expression, 11mm, this matrix MUST contain 14336 rows; otherwise, this matrix MUST contain 4992 rows.If the
obs['in_tissue']
value is1
, then the cell MUST contain at least one non-zero value. If anyobs['in_tissue']
values are0
, then at least one cell corresponding to aobs['in_tissue']
with a value of0
MUST contain a non-zero value.AnnData.raw.X
unless no "normalized" is provided, thenAnnData.X
AnnData.X
The text was updated successfully, but these errors were encountered: