ValueError: zero-size array to reduction operation minimum which has no identity

[shanhuhai-i]

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")`

[ktpolanski]

Please perform the commands one at a time and identify where things go wrong. Please ensure everything completes successfully before proceeding to the next step - the demo notebook inspects the adata as it goes along, so you have some hints as to what you should be seeing. The fact your paths start with /bio looks kind of strange to me but I don't know your system.