Sample image and/or code
Find the raw image here: CP_issues/20210129-toxin16A-p02-m2X_A09.TIF at 6f3b16c2ac71f11682891b17f28d941f4a769b07 · tcrombie/CP_issues · GitHub
- Clone the CP_issues repo found here: GitHub - tcrombie/CP_issues: Reproducible CP issues
- Open CP_issues/short_worms/short_worm_example.cpproj in CellProfiler-4.0.7
- configure input/outputs for your machine and analyze.
- The example image is from an experiment testing the effect of toxins on C. elegans. The nematodes in the well image are sick due to toxin exposure and some are very small. I made a worm model from small sick worms called MDHD.xml (CP_issues/short_worms/input/MDHD.xml) that can identify the smaller worms in this well. However, occasionally the model identifies worms that are extremely small. For example, the output from the pipeline contains worms with Worm_Length of 2 (CP_issues/short_worms/output/output_data/OverlappingWorms_MDHD.csv).
I want to measure the lengths of nemtodes in the well. Note, I am not concerned about larger worms being separated into two worms by the MDHD.xml model. I am more interested in removing the very short, fat worms that are clearly not worms but debris in the well. You can see the worm outlines I’m referring to in the output image here in blue: CP_issues/20210129-toxin16A-p02-m2X_A09_overlay.png at 6f3b16c2ac71f11682891b17f28d941f4a769b07 · tcrombie/CP_issues · GitHub
- I do not understand how the MDHD.xml worm model finds worms of length 2 when
min-path-lengthparameter is set to 31.77 (see MDHD.xml for details).
- How should I interpret the worm model parameters in the MDHD.xml file? Specifically how do these parameters influence the minimum length of a worm. The values below are taken directly from my MDHD.xml file.
<min-area>143.49699999999999</min-area> <max-area>705.5</max-area> <cost-threshold>66.58667600021171</cost-threshold> <num-control-points>21</num-control-points> <max-skel-length>127.1088136726586</max-skel-length> <min-path-length>31.772433103515787</min-path-length> <max-path-length>139.81969503992448</max-path-length> <median-worm-area>428.5</median-worm-area> <max-radius>4.0</max-radius> <overlap-weight>5.0</overlap-weight> <leftover-weight>10.0</leftover-weight> <training-set-size>100</training-set-size>
- Does the fact that I made the model with CP3.1.9 affect how it is run with CP4.0.7?