I’m trying to design a pipeline to identify the spindle-shaped cells (fibrocytes) in the image included in this post. I’ve tried the worm toolbox, with some success, but I still seem to be getting inconsistent counting of these spindle shaped cells.
The image included in this post contains both fibrocytes and macrophages. Macrophages are more circular cells, and cell profiler has no problem counting these cells with a single identifyobjects module. It’s the spindle-shaped fibrocytes that are giving me trouble.
I’d like cellprofiler to recognize the spindle shaped fibrocytes, count the fibrocytes, and then measure their images intensity. **All I’m missing right now is a reliable way to get cell profiler to identify these spindle-shaped, long, thin cells. **
I’ve considered two methods of counting these cells. First, I could stick with the cell profiler worm counting pipeline I’ve been adjusting. Second, I could train cellprofiler-analyst to detect these cells.
What I’m asking is whether anyone has any advice as to which of these two methods to count these spindle-shaped cells would be the simplest. If the cellprofiler analyst option turns out to be the better choice, how would I go about setting up a properties file, object table, and training set? Is there a very beginner walkthrough for how to get started with cell-profiler analyst?
I’ve included a couple of sample pipelines I’ve been working on.