Software plugins for automatic cell counting in the Drosophila central nervous system

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DeadEasy_Central_Brain_Forero_Hidalgo.ijm

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DeadEasy_Dopaminergic3DNew_Forero_Hidalgo.ijm

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Cells_filter_Forero-Hidalgo.java

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DEADEASY OPTIC LOBE.zip

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DeadEasy ADULT Kenyon Cells.zip

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DeadEasy_GliaAdult.ijm.txt

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README1213-Instructions.txt

readme archive 616 disk0/00/00/12/13 2025-01-13 16:16:11 2025-01-14 11:57:23 2025-01-13 16:16:11 data_collection show Forero Manuel Guillermo manuel.forero@ibague.edu.co 0000-0001-9972-8621 Hidalgo Alicia a.hidalgo@bham.ac.uk 0000-0001-8041-5764 Software plugins for automatic cell counting in the Drosophila central nervous system 10col_life Drosophila; adult brain; cell counting; larval; cell number; synapse; central nervous system; NMJ; adult brain; larva; embryo; nuclei; neurons; glia; apoptotic cells; Caspase-3; Dcp1; HB9; Brp; Repo; Histone-YFP; pHistone-H3; pH3 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 DeadEasy Central Brain: first published in Li et al (2020) eLife 9:e52743. https://doi.org/10.7554/eLife.52743 Published also in: Sun et al (2024) eLifeeLife13:RP102222 https://doi.org/10.7554/eLife.102222.1 DeadEasy Dopaminergic neurons: Published in: Sun et al (2024) eLife13:RP102222 https://doi.org/10.7554/eLife.102222.1 2025-01-13 published University of Birmingham https://doi.org/10.25500/edata.bham.00001213 Software research-data@contacts.bham.ac.uk School of Biosciences wt 223197/Z/21/Z yes yes yes TRUE PI Hidalgo Alicia a.hidalgo@bham.ac.uk A Toll-receptor map underlies structural brain plasticity pub https://doi.org/10.7554/eLife.52743 Documents A neurotrophin functioning with a Toll regulates structural plasticity in a dopaminergic circuit pub https://doi.org/10.7554/eLife.102222.3 Documents Software from the Hidalgo lab web https://www.biosciences-labs.bham.ac.uk/hidalgo/Software.html IsCitedBy Laser scanning confocal microscopy data were acquired from Drosophila fixed embryos and fixed and dissected larvae and adult brains. Cells were labelled either with antibodies or nuclear reporters (eg UAS-HistoneYFP). The development of the plugins involved multiple rounds of optimisation (details of this have been published already). Laser scanning confocal microscopy data used to generate all of the DeadEasy plugins were acquired from 2004 onwards until 2024, and the microscopy data were contributed by many different members of the Hidalgo Lab over this period. en 2004 2024