DeadEasy Neurons is an imageJ plug-in allows you to count automatically neuronal nuclei stained with HB9 in whole Drosophila embryos. The plug-in was optimised to run with stacks of images with 0.245*0.245*0.245 cubic micron voxels.
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Forero MG, Pennack JA, and Hidalgo A. (2010)
DeadEasy neurons: Automatic counting of HB9 neuronal nuclei in Drosophila.
Cytometry, 77A: 371–378. doi: 10.1002/cyto.a.20877