Video tutorials on how to use CellProfiler Analyst CellProfiler 2.1 tutorial Pipelines 1–4 (zip).Digitally align worms, select orientation (heads or tails up).A worm model (DefaultWormModel.xml or a new model created by Pipelines 2 and 3) is needed as input for the straightening step. This pipeline loads the untangling results from Pipeline 1 and allows the user to edit any errors in the untangling prior to straightening the worms for visualization and extraction of measurements. Pipeline 4: Untangle, correct, and straighten worm clustersĬellProfiler 2.1 pipeline- Pipeline4_Manuall圜orrectStraighten.cppipe The pipeline is fully automated, and the resulting model will be called MyWormModel.xml. It is recommended to visually browse through the binary input images before running this pipeline to make sure that they represent single worms. This module takes the manually selected training worms from Pipeline 2 as input. ![]() Pipeline 3: Create a new worm model from individual wormsĬellProfiler 2.1 pipeline- Pipeline3_TrainModel.cppipe The correct input for that module is SelectedSingleWorms. NOTE: The video incorrectly states that WormObjects should be used as input for the ConvertObjectsToImage module. Make sure that the selected single worms are saved as training worms.Approximately 50 worms representing the variability in the dataset is usually sufficient. Manually select single worms for worm modeling.Pre-process data by compensating for non-uniform illumination and removing artifacts such as well edges and bubbles.This pipeline requires manual interaction selecting representative non-touching worms. Steps A-C are the same as in Pipeline 1 the same pre-processing and foreground/background segmentation should be applied both when creating the worm model and when running the analysis as changes to the pre-processing may affect the appearance of the width of the worms, in turn influencing the model. DefaultWormModel.xml provided with Pipeline 1) fits the new data. This pipeline may be omitted if a previously created model (e.g. Pipeline 2: Find, select, and save individual wormsĬellProfiler 2.1 pipeline- Pipeline2_SelectSingleWorms.cppipe Export measurements to an SQLite database, save worm segmentation masks and images of worm and fat outlines.Identify sub-regions (fat) and extract measurements.Straighten worms and extract measurements.Identify individual worms by worm untangling and extract measurements.Separate worms and worm clusters the from image background by foreground/background image segmentation. ![]()
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