I am trying to analyse the changes in stromal cells in T-Cell lymph nodes during infection and I was wondering if there is a way to get cell profiler to count the number of branches a cell gives off?



This is not currently a measurement that CellProfiler makes. My guess is that sometime by the end of the year it might be a new added feature, but for now you are out of luck. If you, or your local Matlab gurus, want to make a MeasureBranches module please feel free to do so and donate the code to the project!

You could use the skeletonize option (‘skel’) in the Morph module as a starting point - after running this module on the objects (you might need to run ConvertToImage to convert objects into a binary image first) you just need to measure how many ‘ends’ or ‘tips’ the skeleton has. That is currently the missing piece you would need.


For those who are interested: CellProfiler 2.0 (available from our website) has a new module called MeasureNeurons, which measures the number of trunks and branches for each neuron in an image. It takes a skeletonized image of the neuron plus previously identified seed objects (for instance, the neuron soma) and finds the number of axon or dendrite trunks that emerge from the soma and the number of branches along the axons and dendrites.

Despite the name, this module may be used for any cell type as long as the phenotype is similar and you are generate the required input images.