Closed BioMedMS closed 1 year ago
I have found the issue now. It had actually nothing to do with the installation. I just used an existing pipeline from another cellprofiler installation on another system, which uses a slightly different version and it seems like these two versions are not compatible with each other. Making the same pipeline from scratch at the new installation solved the issue.
Hi everybody,
I am trying to run the runstardist module with cellprofiler. But i get the following TypeError when I add the stardist module:
OS: windows server 2012 R2 Python 3.8.10 cellprofiler 4.2.4 (installed with pip) stardist 0.8.3 During the installation process I got a dependency error with pip since stardist wants to have h5py < 3 and cellprofiler wants h5py==3.6.0. I am currently using h5py 3.6.0 but the same error appears with h5py 2.1.0 (which is the one stardist wants to have)
Can anybody help me with this?
P.S: Unfortunately I can't move the Cellprofiler installation to the C: drive because we are not allowed to install anything on that drive.
This is my package list:
absl-py==1.3.0 astunparse==1.6.3 boto3==1.26.3 botocore==1.29.3 cachetools==5.2.0 cellpose==2.0.5 CellProfiler==4.2.4 cellprofiler-core==4.2.4 centrosome==1.2.1 certifi==2022.9.24 charset-normalizer==2.1.1 colorama==0.4.6 csbdeep==0.7.2 cycler==0.11.0 deprecation==2.1.0 docutils==0.15.2 fastremap==1.13.3 flatbuffers==2.0.7 future==0.18.2 gast==0.4.0 google-auth==2.14.0 google-auth-oauthlib==0.4.6 google-pasta==0.2.0 grpcio==1.50.0 h5py==3.6.0 idna==3.4 imagecodecs==2022.9.26 imageio==2.22.4 importlib-metadata==5.0.0 inflect==6.0.2 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.2.0 keras==2.7.0 Keras-Preprocessing==1.1.2 kiwisolver==1.4.4 libclang==14.0.6 llvmlite==0.39.1 mahotas==1.4.13 Markdown==3.4.1 MarkupSafe==2.1.1 matplotlib==3.1.3 mysqlclient==1.4.6 natsort==8.2.0 networkx==2.8.8 numba==0.56.4 numpy==1.23.4 oauthlib==3.2.2 opencv-python-headless==4.6.0.66 opt-einsum==3.3.0 packaging==21.3 Pillow==9.3.0 prokaryote==2.4.4 protobuf==3.19.6 psutil==5.9.3 pyasn1==0.4.8 pyasn1-modules==0.2.8 pydantic==1.10.2 pyparsing==3.0.9 python-bioformats==4.0.6 python-dateutil==2.8.2 python-javabridge==4.0.3 PyWavelets==1.4.1 pyzmq==22.3.0 requests==2.28.1 requests-oauthlib==1.3.1 rsa==4.9 s3transfer==0.6.0 scikit-image==0.19.3 scikit-learn==1.1.3 scipy==1.9.3 sentry-sdk==0.18.0 six==1.16.0 stardist==0.8.3 tensorboard==2.10.1 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.1 tensorflow==2.7.0 tensorflow-estimator==2.7.0 tensorflow-io-gcs-filesystem==0.27.0 termcolor==2.1.0 threadpoolctl==3.1.0 tifffile==2022.4.8 torch==1.13.0 tqdm==4.64.1 typing-extensions==4.4.0 urllib3==1.26.12 Werkzeug==2.2.2 wrapt==1.14.1 wxPython==4.1.0 zipp==3.10.0