cpproj file stores collected information using the HDF5įormat. See File >įor those interested, some technical details: Example:You have several image stacks representing 3D structures in the following format: The stacks are saved in. general, we recommend saving stacks and movies in. You also have the option of automatically saving the associated pipelineįile and the file list in addition to the project file. CellProfiler uses the Bio-Formats library for reading various image For more details on supported files, see this webpage.
cppipe, by selecting File > Export > Pipeline.cppipe files contain only the list of steps and their corresponding settings and do not contain information about images. Project, complete with the current image file list and pipeline, to aĪs an alternative, you can save the pipeline by itself to a file with the extention. Here, the directory is set to the folder Output in the current working directory (ensure that the folder exists). In the Python integration, the default output can be configured in the preferences. You can always save your current work to a new projectįile by selecting File > Save Project As…, which will save your The default output directory of the CellProfiler Python package is C:Users USERNAME.
There is no need to save it unless you are saving the project to a new Pkg_resources.ContextualVersionConflict: (matplotlib 1.5.1 (/usr/lib/python2.7/dist-packages), Requirement.parse('matplotlib>=2.0.As you work in CellProfiler, the project is updated automatically, so Raise VersionConflict(dist, req).with_context(dependent_req)
Return cls._build_from_requirements(_requires_)įile "/usr/local/lib/python2.7/dist-packages/pkg_resources/_init_.py", line 593, in _build_from_requirementsįile "/usr/local/lib/python2.7/dist-packages/pkg_resources/_init_.py", line 786, in resolve Cell profiler seems to be running using python2.7, not python3.6 which is also set up on this machine, so this could be the source of the problem?Įrror message in full: Traceback (most recent call last):įile "/usr/local/bin/cellprofiler", line 6, in įrom pkg_resources import load_entry_pointįile "/usr/local/lib/python2.7/dist-packages/pkg_resources/_init_.py", line 3112, in "/usr/local/lib/python2.7/dist-packages/pkg_resources/_init_.py", line 3096, in _call_asideįile "/usr/local/lib/python2.7/dist-packages/pkg_resources/_init_.py", line 3125, in _initialize_master_working_setįile "/usr/local/lib/python2.7/dist-packages/pkg_resources/_init_.py", line 580, in _build_master Our introduction to automated image analysis principles and practicalities is published as an educational article at PLoS.
#Cellprofiler save movie not working software
However when I attempt to run cellprofiler from terminal, i encounter the following error code, which seems to be telling me there is a version conflict of matplotlib. Technical descriptions of CellProfiler and CellProfiler Analyst software can be found in our papers while more written tutorials can be found on the CellProfiler GitHub page. Im trying to run the bioimaging analysis package 'cell profiler' on Ubuntu 16.04, following the source installation instructions provided by the developers:
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