Cell Counting

A workflow in Python to measure muscule fibers corresponding to the method used in Keefe, A.C. et al. Muscle stem cells contribute to myofibres in sedentary adult mice. Nat. Commun. 6:7087 doi: 10.1038/ncomms8087 (2015).

Example image:

muscleQNT/15536_2032_0.tif ...

Estimate the frequency of hepatitis C virus infected cells based on the intensity of viral antigen associated immunofluorescence. 

The core is an ImageJ Macro, so it's easy to modify for one's own needs (Link to the code). 

An ImageJ plugin (author: Kurt De Vos) for counting multiple cell classes manually, which overlays already-counted cells on the image. It is controlled via its own graphical user interface, and can export and load results.