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CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
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Problems with installing runstardist in Cellprofiler #170

Closed BioMedMS closed 1 year ago

BioMedMS commented 1 year ago

Hi everybody,

I am trying to run the runstardist module with cellprofiler. But i get the following TypeError when I add the stardist module:

Traceback (most recent call last):
File "e:\jan\projects\fiscas\fiscas-venv\lib\site-packages\cellprofiler\gui\pipelinelistview.py", line 1069, in __on_i
tem_activated
self.__module_view.set_selection(module.module_num)
File "e:\jan\projects\fiscas\fiscas-venv\lib\site-packages\cellprofiler\gui\module_view_module_view.py", line 363, in
set_selection
control = self.make_choice_control(
File "e:\jan\projects\fiscas\fiscas-venv\lib\site-packages\cellprofiler\gui\module_view_module_view.py", line 726, in
make_choice_control
choices = choices + [v.value]
TypeError: can only concatenate tuple (not "list") to tuple
Exiting the pipeline validation thread

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

BioMedMS commented 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.