All details regarding the settings on how to optimise the stainings and acquisition for optimal results are provided in the following publications from the Hidalgo Lab: Adult brain: Sun et al (2024) eLife 13:RP102222 Li et al (2020) eLife 9:e52743 Larvae cells: Forero, Kato and Hidalgo (2012) J Microscopy 246(2):202-12 Kato, Forero and Hidalgo (2011) PLoS Biology 9, e1001133 Larvae synapse with anti-Brp: Sutcliffe et al (2013) PLoS One 8(10):e75902 Ulian- Benitez et al (2017) PLoS Genetics 13(8): e1006968 Embryos: Forero and Hidalgo (2011) Advanced biomedical engineering. Intech Open Access Publisher, pages 183-204 Forero et al (2010) PLoS One 5, e10557 Forero, Pennack, Hidalgo (2010) Cytometry Part A 77A, 371-378 Forero et al (2009) PLoS One 4, e5441.
These plugins work with ImageJ not Fiji. See further details also here: https://www.biosciences-labs.bham.ac.uk/hidalgo/Software.html