Raise VersionConflict(dist, req).with_context(dependent_req) After optimization of the CellProfiler pipeline. most well known is CellProfiler Analyst (CPA) (Jones et al., 2009). Prune at 22:29 Add a comment 1 Answer Sorted by: 1 The error is as it says, it is unable to allocate memory, because there isn't enough. between the training and test error, the model is experiencing. 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 To overcome the limitation of on-site test data, researchers generally adopt three-dimensional numerical simulation methods to conduct the back analysis of the in situ stress field in the engineering field 10,11,12,13. We recently developed open-source image analysis software, CellProfiler, which measures a rich set of cellular features in images, such as size, shape, and staining patterns including intensity, texture, and colocalization 4, 5. CellProfiler accurately segmented the colonies within the images (Figure 13). 13 1 2 1 Where are you confused The error message seems clear: you're trying to allocate 137Mb of data, and you don't have that available. 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. More information can be found in the CellProfiler Wiki.
#Cellprofiler analyst error 13 software#
Im trying to run the bioimaging analysis package 'cell profiler' on Ubuntu 16.04, following the source installation instructions provided by the developers: 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.
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