OSError: libopenslide.so.0: cannot open shared object file: No such file or directory

[OnkarMulay]

python3 -m stnet prepare spatial

On running this command I have got this error, any idea how should I tackle this...?? File not found, where can I download it from?

Thanking for the help in advance

[chenyang1999]

Maybe you need to preprocess the dataset, I wrote a code to preprocess it and put it under ./data

import os
import glob
file_path="./hist2tscript"
for img in glob.glob(file_path+"/*"):
    if "HE_" in img:
        fn=img.replace("HE_","")
        command=f"mv {img} {fn}"
        print(command)
        os.system(command)
    if "_stdata" in img:
        fn=img.replace("_stdata","")
        command=f"mv {img} {fn}"
        print(command)
        os.system(command)
    if "spots" in img:
        fn=img.replace("spots_","").replace(".csv",".spots.txt")
        command=f"mv {img} {fn}"
        print(command)
        os.system(command)
file_list=glob.glob(file_path+"/*.jpg")
# print(file_list)
sample_id=[]
for f in file_list:
    sample_id.append(f.split("/")[-1].split(".")[0].split("_")[0])
# print(sample_id)
# sample_id=[x[2:] for x in sample_id]
print(sample_id)
# print(glob.glob(file_path+"/*"))
for sid in sample_id:
    print(sid)
    temp_path=file_path+"/BRCA/"+sid
    print(temp_path)
    os.makedirs(file_path+"/BRCA/"+sid,exist_ok=True)
    for f in glob.glob(file_path+"/*"):
        if sid[2:] in f:
            print(f)

            command=f"mv {f} {temp_path}"
            print(command)
            os.system(command)

for img in glob.glob(file_path+"/*/*/*"):
    patient_id=img.split("/")[-2]
    # print(patient_id)
    stdata = img.split("/")[-1]
    # print(stdata)
    if patient_id not in stdata:
        fn=img.replace("BC","BT")
        command = f"mv {img} {fn}"
        print(command)
        os.system(command)

[chenyang1999]

BUT, I still lack "*_croods.tsv", if anybody has a solution? @OnkarMulay

[OnkarMulay]

I am trying running it manually not using any functions

[Greywan]

run sudo apt install python-openslide

[andrewbrown1022]

Thanks @chenyang1999, I am also missing the "_Coords.tsv". @bryanhe any chance you could provide it? Thank you!

[chenyang1999]

@andrewbrown1022 我没有这个肿瘤标记数据,我现在是直接拿全部 spots 的基因表达训练

[DecodeGenome]

I got the same error message " OSError: libopenslide.so.0: cannot open shared object file: No such file or directory " after run "python3 -m stnet prepare spatial" command at virtual env python3. I also preprocess the images in ./data/hist2tscript" as suggested here by chanyang1999, the same error. Any one has suggestions?

[Wmoonquaker]

I have solved it by running "sudo apt-get install libopenslide-dev".