README1213-Instructions

DeadEasy Central Brain: this ImageJ plugin counts automatically the number of sparsely distributed labelled nuclei within the central brain of adult Drosophila, and acquired as laser scanning confocal microscopy images. It works optimally with UAS-Histone-YFP for which it was developed. It works as an ImageJ plug-in (not Fiji!!!). The confocal settings are important, to get the settings for which it was developed check Li et al (2020) eLife. DeadEasy Optic Lobes: this ImageJ plugin counts automatically the number of sparsely distributed labelled nuclei within the optic lobes of adult Drosophila, and acquired as laser scanning confocal microscopy images. It works optimally with UAS-Histone-YFP for which it was developed. It works as an ImageJ plug-in (not Fiji!!!). The confocal settings are important, to get the settings for which it was developed check Li et al (2020) eLife. DeadEasy Dopaminergic neurons: this ImageJ plugin counts automatically the number of dopaminergic PAM cells labelled with anti-TH, within the central brain of adult Drosophila, and acquired as laser scanning confocal microscopy images. It works well in controls, but less well in other genotypes, depending on the phenotype. In these cases, it is useful to run it first, and then edit the cell counts manually. It works as an ImageJ plug-in (not Fiji!!!). The confocal settings are important, to get the settings for which it was developed check Sun et al (2024) eLife. DeadEasy adult glia: this ImageJ plugin counts automatically the number of labelled glial nuclei within the whole adult Drosophila brain, and acquired as laser scanning confocal microscopy images. It works optimally with anti-Repo and also UAS-Histone-YFP for which it was developed. It works as an ImageJ plug-in (not Fiji!!!). The confocal settings are important, to get the settings for which it was developed check Li et al (2020) eLife and Singh et al (2025). DeadEasy Kenyon cells: this ImageJ plugin counts automatically the number of Kenyon cell labelled nuclei within the central brain of adult Drosophila, and acquired as laser scanning confocal microscopy images. It works optimally with UAS-Histone-YFP for which it was developed. It works as an ImageJ plug-in (not Fiji!!!). The confocal settings are important, to get the settings for which it was developed check Li et al (2020) eLife. Cells: required to run the above. If any macro fails, load the DeadEasy Full set for embryo & larvae. DeadEasy Full set embryo & larvae: this set contains multiple ImageJ plugins and required macros to count automatically the number of sparsely distributed labelled nuclei within the central brain of Drosophila embryos and larvae, and acquired as laser scanning confocal microscopy images. It works optimally with: (1) DeadEasy Caspase for anti-Caspase or Dcp1 (2) DeadEasy neurons: for anti-HB9 stainings or similar (3) DeadEasy mito-glia: for anti-Repo or anti-pH3 in embryos (4) DeadEasy Larval glia: for anti-Repo, anti-pH3 and UAS-Histone-YFP in larvae (5) DeadEasy synapse: for anti-Brp in larval NMJ. All of these plugins work as an ImageJ plug-in and do not work with Fiji. The confocal settings are important, to get the settings for which they were developed and how to modify them and validate them see the publications listed below.