Software from the Hidalgo lab   

Please download freely the software we have developed, to be used as ImageJ plug-ins. They work best with ImageJ143.zip - download!

DeadEasy Caspase for embryonic CNS

Published in: Forero MG, Pennack JA, Learte AR and Hidalgo A. (2009) DeadEasy Caspase: automatic counting of apoptotic cells in Drosophila. PLoS One 4(5): e5441. doi:10.1371/journal.pone.000544.

 Installation: Download the DeadEasy Caspase.zip, unzip the folder and copy it following the structure of the DeadEasyCaspase folder:

Copy the files in the downloaded 'Plugins' folder to the ImageJ plugins folder, and the files in the 'Macros' to the ImageJ macros folder; restart ImageJ; there will be two new commands in the ImageJ Plugins menu called "DeadEasy Caspase" and "Lots-DeadEasy Caspase" and another one in the ImageJ Macros also called "DeadEasy Caspase".

 Compilation: Download the DeadEasy Caspase.zip, unzip the folder and copy it following the structure of the DeadEasyCaspase folder. Compile and run using Plugins/Compile and Run. Restarting ImageJ will add a "Lots-DeadEasy Caspase" command to the Plugins menu.

 Description: This plug-in allows you to count automatically apoptotic cells stained with anti-cleaved-Caspase-3 in whole Drosophila embryos. It was developed and validated for the embryo only, and we subsequently modified this programme to count dying cells in the larva (see below). The plug-in was optimised to run with stacks of images with 0.25*0.25*0.25 cubic micron voxels.

For further details see the paper Forero et al.

Source: Included in DeadEasy Caspase.zip

 

DeadEasy Caspase for larval CNS

Published in: Kato, Forero and Hidalgo (2011) The glial regenerative response to CNS injury is enabled by Pros-Notch ad Pros-NFkB feed-back. PLoS Biology 9, e1001133

Instal as above, download:

This version has been specifically optimised to count Caspase positive cells in the larva. For details see publication above.

DeadEasy Neurons

Published in: Forero MG, Pennack JA, and Hidalgo A. (2010) DeadEasy neurons: Automatic counting of HB9 neuronal nuclei in Drosophila. Published Online: Feb 16 2010. doi: 10.1002/cyto.a.20877

 Installation: Download the DeadEasy Neurons.zip, unzip the folder and copy it following the structure of the DeadEasyNeurons folder:

Copy the files in the downloaded 'Plugins' folder to the ImageJ plugins folder, and the files in the 'Macros' to the ImageJ macros folder; restart ImageJ; there will be two new commands in the ImageJ Plugins menu called "DeadEasy Neurons" and "Lots-DeadEasy Neurons" and another one in the ImageJ Macros also called "DeadEasy Neurons".

 Compilation: Download the DeadEasy Neurons.zip, unzip the folder and copy it following the structure of the DeadEasyNeurons folder. Compile and run using Plugins/Compile and Run. Restarting ImageJ will add a "Lots-DeadEasy Neurons" command to the Plugins menu.

 Description: This plug-in allows you to count automatically neuronal nuclei stained with HB9 in whole Drosophila embryos, which are much closer together than glial nuclei. It will however not count all nuclei, but should work with other good nuclear antibodies (e.g. Eve). The plug-in was optimised to run with stacks of images with 0.245*0.245*0.245 cubic micron voxels.

For further details see the paper Forero et al.

Source: Included in DeadEasy Neurons.zip

 

DeadEasy Mito-Glia

Published in: Forero MG, Learte AR, Cartwright S. and Hidalgo A. (2010) DeadEasy Mito-Glia: automatic counting of mitotic cells and glial cells in Drosophila. PLoS One 5(5): e10557. doi:10.1371/journal.pone.0010557.

 

Installation: Download the DeadEasy_Mito-Glia.zip, unzip the folder and copy it following the structure of the DeadEasyMito-Glia folder:

Copy the files in the downloaded 'Plugins' folder to the ImageJ plugins folder, and the files in the 'Macros' to the ImageJ macros folder; restart ImageJ; there will be two new commands in the ImageJ Plugins menu called "DeadEasy Mito-Glia" and "Lots-DeadEasy Mito-Glia" and another one in the ImageJ Macros also called "DeadEasy Mito-Glia".

 Compilation: Download the DeadEasy_Mito-Glia.zip, unzip the folder and copy it following the structure of the DeadEasyMito-Glia folder. Compile and run using Plugins/Compile and Run. Restarting ImageJ will add a "Lots-DeadEasy Mito-Glia" command to the Plugins menu.

 Description: This plug-in allows you to count automatically mitotic cells stained with phospho-Histone-3 in whole Drosophila embryos. The plug-in was optimised to run with stacks of images with 0.25*0.25*0.25 cubic micron voxels.

For further details see the paper Forero et al.

Source: Included in DeadEasy_Mito-Glia.zip

DeadEasy Larval Glia

Published in: Forero, Kato and Hidalgo (2012) Automatic cell counting in vivo in the larval nervous system of Drosophila. J Microscopy. 2012 May;246(2):202-12. doi: 10.1111/j.1365-2818.2012.03608

Installation and compilation: Download theDeadEasy Larvalglia.zip and follow same instructions as for programs above.

Description: This plug-in allows you to count automatically glial cells labelled with anti-Repo in the Drosophila larval nervous system (VNC). The plug-in has been developed and validated for Repo positive nuclei of the larval VNC, but it will most likely work with any other nuclear markers in larval tissues so long as the nuclei are not too close together (i.e. will not count all nuclei).

For further details see Forero et al 2012.

Please note: all our DeadEasy programme work best with version ImageJ143.zip.

DeadEasy Synapse

Published in: Sutcliffe B, Forero MG, Zhu B, Robinson I and Hidalgo A (2013) Neuron-type specific functions of DNT1, DNT2 and Spz at the Drosophila neuromuscular junction. PLoS One, 2013 Oct 4;8(10):e75902. doi: 10.1371/journal.pone.0075902

Installation and compilation: Download theDeadEasy SynapseDeadEasy_nc82.zip.zip and follow same instructions as for programs above.

Description: This plug-in allows you to count automatically synaptic active zones labelled with anti-nc82 in the Drosophila larval neuromuscular junction (NMJ). The plug-in does not count each individual nc82 spot, but rather the total voxel volume occupied in 3D by nc82 signal. We have not tested the programme in other synaptic areas outside the NMJ.

For further details see Sutcliffe et al. 2013.

Please note: all our DeadEasy programme work best with version ImageJ143.zip.

 

FlyTracker

Published in: McIlroy G, Foldi I, Aurikko J, Wentzell JS, Lim MA, Fenton JC, Gay NJ and Hidalgo A (2013) Toll-6 and Toll-7 function as neurotorphin receptors in the Drosophila melanogaster CNS. Nature Neuroscience 16, 1248-1256. doi: 10.1038/nn.3474. 

Installation and compilation: Download the FlyTracker DeadEasy Fly_tracker.zip  and proceed as above.

This plugin allows you to track larvae crawling in a clear agar large petri dish, filmed using a standard cheap video camera.