Pkg_resources.ContextualVersionConflict: (matplotlib 1.5.1 (/usr/lib/python2.7/dist-packages), Requirement.parse('matplotlib>=2.0. Raise VersionConflict(dist, req).with_context(dependent_req) These errors simply mean that CellProfiler doesn’t know how to sort the images you’ve given it, and it can’t process them until it knows how they should be organized. 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 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. We also post guided exercises as part of our educational outreach effort.Im trying to run the bioimaging analysis package 'cell profiler' on Ubuntu 16.04, following the source installation instructions provided by the developers: Simple nuclei identification tutorial ( sample data) (courtesy of the German BioImaging network) Performing a colocalization assay ( relevant example pipeline) Using the Worm Toolbox for image analysis of C. Identifying and measuring cells: Cytoplasm-nucleus translocation assay ( relevant example pipeline)Ĭalculating and applying illumination correction for images ( relevant example pipeline) Identifying, measuring, and classifying yeast colonies ( relevant example pipeline) Using the Input modules in CellProfiler 2.1: Using CellProfiler for Quantitative Image Analysis cpipe file format, also found in the Github repository page, as the. However, if using a later version of CellProfiler, it may be necessary to load the pipelines using the. The NIH has published a introductory chapter of “best practices” for image-based high-content screening (in which CellProfiler is mentioned) as part of the Assay Guidance Manual, and our group has published a more advanced follow-up chapter on image analysis methods. Note: The pipeline detailed below will work on the current versions of both CellProfiler (v4.2.1) and Fiji (v1.53). Our introduction to automated image analysis principles and practicalities is published as an educational article at PLoS. 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. Visit our YouTube playlist for video tutorials on CellProfiler, CellProfiler Analyst, segmentation strategies, how to construct pipelines, and much more.
0 Comments
Leave a Reply. |