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When I run this piece of code, I got an error message, I have no idea. Could you help me?
Thank you~
File "~/lib/python3.10/site-packages/numpy/core/_methods.py", line 44, in _amin return umr_minimum(a, axis, None, out, keepdims, initial, where) ValueError: zero-size array to reduction operation minimum which has no identity
hi,
When I run this piece of code, I got an error message, I have no idea. Could you help me?
Thank you~
File "~/lib/python3.10/site-packages/numpy/core/_methods.py", line 44, in _amin return umr_minimum(a, axis, None, out, keepdims, initial, where) ValueError: zero-size array to reduction operation minimum which has no identity
`
path =" /bio/square_002um/"
source_image_path = "/bio/Visium_HD_Mouse_Small_Intestine_tissue_image.btf"
adata = b2c.read_visium(path, source_image_path = source_image_path)
adata.var_names_make_unique()
sc.pp.filter_genes(adata, min_cells=3)
sc.pp.filter_cells(adata, min_counts=1)
mpp = 0.5
b2c.destripe(adata)
thr = 10
mask = ((adata.obs['array_row'] >= 1450) &
(adata.obs['array_row'] <= 1550) &
(adata.obs['array_col'] >= 250) &
(adata.obs['array_col'] <= 450)
)
bdata = adata[mask]
b2c.scaled_he_image(adata, mpp=mpp, save_path="stardist/he.tiff")`
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