![]() ![]() Python wrapper for the Java Native Interface. Pkg_resources.ContextualVersionConflict: (matplotlib 1.5.1 (/usr/lib/python2.7/dist-packages), Requirement.parse('matplotlib>=2.0. Software for quantitative analysis of biological images - CellProfiler. ![]() What version of CellProfiler should I use We recommend the stable release of CellProfiler. More information can be found in the CellProfiler Wiki. Raise VersionConflict(dist, req).with_context(dependent_req) CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. ![]() 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 Segmentation & CellProfiler- Principles, 2D, and 3D COBA: Center for Open Bioimage Analysis 905 subscribers Subscribe 6.2K views Streamed 2 years ago Show more Live chat replay is not available. When I installed CellProfiler on a Ubuntu 18.04 machine running Python 3.6, I created an virtual environment for CellProfiler with Python 2.7 and installed all required packages into this environment. It’s a bit tricky right now, because CellProfiler requires Python 3.8+, and CellPose requires Python 3.4-3.7, but if our Python versions ever align, we can certainly see why it would be useful 1 Like DStirling (David Stirling) August 26, 2021, 6:04pm 10 Here we go This should be much simpler going forwards. 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 Requires: Python >3.8 Maintainers 0x00B1 aether alicelucas bcimini DavidStirling gnodar01 Classifiers. 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. 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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