This is my first question on image.forum. The tutorial on the CellProfiler website and the answers here helped me a lot.
I would like to analyze our images to determine live/dead nematodes using Worm Toolbox Pipelines.
I modified the “Worm_Analysis_CreateWormModel.cppipe” pipeline and create a new pipeline “TrainingModel.cpproj” to use our data. Also, I modified the “Worm_Analysis_UntangleWormsAndMakeMeasurements.cppipe” to the new pipeline “RunAssaaySolidity.cpproj”. Windows10 system and CellProfiler version 2.1.0 were used.
Please see the attached files of the pipelines and images.
Unfortunately, we have challenged images, with a lot of aggregates in the growing media. The result of this model was that the worms were divided into 3-4 parts. In addition, it was a problem to distinguish between the worms and the aggregates.
I didn’t succeed to improve the thresholding and the segmentation.
Is it possible to improve these pipelines?
Thank you in advance.
C2_IX_Trans_T81_Z0.ome.tif (2.8 MB) C3_IX_Trans_T61_Z0.ome.tif (2.8 MB) C4_IX_Trans_T61_Z0.ome.tif (2.8 MB) C6_IX_Trans_T61_Z0.ome.tif (2.8 MB) C9_IX_Trans_T61_Z0.ome.tif (2.8 MB) MyNewWormModel.xml (25.1 KB) RunAassay.cpproj (157.3 KB) TrainingModel.cpproj (485.3 KB)