Result = self]įile "/Users/bcimini/Documents/GitHub/CellProfiler/core/cellprofiler_core/utilities/hdf5_dict.py", line 435, in _getitem_Īssert feature_exists, "Feature does not exist". Vals = self.hdf5_dictįile "/Users/bcimini/Documents/GitHub/CellProfiler/core/cellprofiler_core/utilities/hdf5_dict.py", line 430, in _getitem_ As a result colour/multichannel images dont display properly in CPA out of the box. OSX 12.6, 4.2.4&4.2.5 built, 4.2.x source branch Windows 4.2.5 builtįailed to complete post_run processing for module ExportToDatabase.įile "/Users/bcimini/Documents/GitHub/CellProfiler/core/cellprofiler_core/pipeline/_pipeline.py", line 1535, in post_runįile "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/modules/exporttodatabase.py", line 2857, in post_runįile "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/modules/exporttodatabase.py", line 4148, in write_properties_fileĪll_properties = self.get_property_file_text(workspace)įile "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler/cellprofiler/modules/exporttodatabase.py", line 4421, in get_property_file_textĬhannels_list = _measurement("ExportToDb", "ExportToDb_Channels")įile "/Users/bcimini/Documents/GitHub/CellProfiler/core/cellprofiler_core/measurement/_measurements.py", line 854, in get_measurement properties file with ExportToDatabase, CellProfiler currently assumes that all input images are single channel. Run the QC tutorial at ĭesktop (please complete the following information): I assume we tested at the time that #4396 worked, but I can't get it to work in a couple of test cases in my hands, including CP 4.1.3. Conversely, during the run we have access to the. In both of these phases we have access to the image names, but not their dimensionality. CellProfiler insists on creating the properties file in the pre-run phase and the post-run phases. As far as I can tell, this measurement IS correctly written into the measurement tables during the run, but in the post_run (where the properties file is made, it's done. To generate the properties file correctly, we need to know how many channels each selected image contains. Plate Viewer displays data according to the. Classifier enables cell and field-of-view-level classification of multiple phenotypes using popular supervised machine learning models. It turns out it's due to not checking in that part of the code path whether the "ExportToDb", "ExportToDb_Channels" measurement was made - that measurement was added in #4396. CellProfiler Analyst’s primary tools: Image Gallery displays (full and cell) images with a variety of filter options and can be used interactively with other tools. In addition to performing image analysis to generate measurements. Excel (Microsoft) is a general business comercial package, whereas Prism (Graphpad) is a commercial program tailored towards research scientists for statistical analyses. H/T using ExportToDatabase in a situation where the user wants to specify which channels are used in the properties file and/or which color they're assigned (aka where Include information for all images, using default values? is No), in certain circumstances, ExportToDatabase failed with the stack trace below. Cellprofiler properties file software Calc (LibreOffice) is open-source software and freely-available.
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