This model could either be the DefaultWormModel.xml provided above, or a new worm model created by pipelines 2 and 3 above. This is the main pipeline for delineating worms (also those in clusters) and extracting different kinds of shape and intensity measurements. Pipeline 1: Identify and collect measurements from individual worms and sub-regionsĬellProfiler 2.1 pipeline- Pipeline1_UntangleWormsExtractMeasurements.cppipe Note that CellProfiler 2.1 should be used. All measurements are exported to a database for further exploration and phenotyping. may also be extracted from individual worms after manual correction. Measurements, such as intensity of stain, fat stain distribution, fat region size, worm width etc. due to a different image resolution or different worm strain), a new worm model can be created using Pipeline 2 (pink) to (g) manually select non-touching worms making up a training set for a new model built by Pipeline 3.įor low-throughput experiments, it is possible to manually curate faulty segmentation results using Pipeline 4 (orange) by (h) manual editing of the output from step d of pipeline 1, and (i) manual flipping of digitally straightened worms so that they all align in with heads or tails up. If the provided default worm model does not fit the input data (e.g. Once worms and fatty regions are identified, a large number of intensity, shape and texture measurements are extracted. Now, each individual detected worm has a unique color.ĭigitally straighten worms and align them to a simple worm atlas for measurement of stain distribution.ĭetect fatty regions within worms. Individual worms/worm clusters are randomly colored.ĭelineate individual worms by model-based worm untangling.
Pre-process to detect artifacts such as bubbles and well edges.ĭetect worms and clusters of worms. The main analysis pipeline, Pipeline 1, shown in blue, is fully automated, and consists of the following steps:
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