enhanced_exp_adata.X is NA

[travell1993]

Thank you very much for your software. However, when I used tissue_hires_image. png as the input image, The results of enhanced_exp_1data.X are all NA. After consulting the community tutorial, I understand that this is due to a mismatch between the image and location information. I would like to know if it is necessary to use images from. tif files in order to run your software? If there is only the tissue_hires_image. png file, what kind of processing does it need to go through?

[wuxiangning]

hello! have u solve this issue?

[xiaomaoxilian]

hello! Before generating the h5ad file, you can adjust pixel_x and pixel_y coordinates by multiplying them with the corresponding magnification factor found in the accompanying document.

[wuxiangning]

well.I did this, but this error still present.can u give us u code please?
Thank u very much!

[xiaomaoxilian]

from scanpy import read_10x_h5

adata = read_10x_h5("../data/filtered_feature_bc_matrix.h5")
spatial=pd.read_csv("../data/tissue_positions_list.csv",sep=",",header=None,na_filter=False,index_col=0)
adata.obs["x1"]=spatial[1]
adata.obs["x2"]=spatial[2]
adata.obs["x3"]=spatial[3]
adata.obs["x4"]=spatial[4]*0.12207031
adata.obs["x5"]=spatial[5]*0.12207031
adata.obs["array_x"]=adata.obs["x2"]
adata.obs["array_y"]=adata.obs["x3"]
adata.obs["pixel_x"]=adata.obs["x4"]
adata.obs["pixel_y"]=adata.obs["x5"]
#Select captured samples
adata=adata[adata.obs["x1"]==1]
adata.var_names=[i.upper() for i in list(adata.var_names)]
adata.var["genename"]=adata.var.index.astype("str")
adata.write_h5ad("../data/colo4_data.h5ad")```


Hope these codes can help u.