![]() The pipeline can be modified to replace the operations in red with other steps and the pipeline re-uploaded to fix this problem. Red boxes indicate incompatible operations that could not be modified and will render the pipeline non-executable. ![]() You will test your pipeline on a few images so that you can optimize the settings. Green boxes indicate regular CellProfiler modules that were kept unchanged. You will set up a CellProfiler pipeline consisting of a number of modules each module performs a unique image-processing step, and multiple modules can be arranged such that they are executed in sequential order. Certain operations (such as Crop in this example) are not currently compatible with BisQue and are ignored without affecting the rest of the pipeline. The next three steps in the pipeline are shown in transparent color to indicate that they were inactivated. These pipeline conversions happen automatically when the pipeline is uploaded into BisQue. File cellprofiler\pipeline.pyc, line 1956, in runimageset File cellprofiler\pipeline.pyc, line 2067, in runmodule File cellprofiler\modules\applythreshold.pyc, line 139, in run File cellprofiler\modules\identify.pyc, line 864, in thresholdimage File cellprofiler\modules\identify. are accessible in the main menu of CellProfiler and allow you to plot, view, or export your measurements (e.g., to Excel). Examine the measurements using Data tools. Click the Analyze Imagesbutton to start processing. We won’t be using the results data from this run so which set of images is not important, what matters is that we can run the pipeline workflow from start to end. main menu of CellProfiler, or drag and drop it to the pipeline window. In CellProfiler, a project is comprised of two elements: An image file list which is the list of files and their locations that you select as candidates for analysis. For example, the first box ( BisQueLoadImages) is shown in blue to indicate that the original module(s) from the pipeline have been replaced with a BisQue specific component that allows to read images directly from BisQue. Open up the CellProfiler pipeline you previously used to perform the analysis, then remove all but a single set of images. sAreaShape ontains only h CellProfiler pipeline ut folders se. ![]() Note that some boxes have different colors. Advanced algorithms for image analysis are available as individual modules that can be placed in sequential order together to form a pipeline the pipeline. he CellProfile cellprofiler.o ad CellProfile.
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