Cachero S, Ostrovsky AD and Jefferis GS (2012)\\
A mutual information approach to automate identification of neuronal clusters in Drosophila brain images.\\
Front. Neuroinform. 6:21. doi: [[http://dx.doi.org/10.3389/fninf.2012.00021|10.3389/fninf.2012.00021]]

The main documentation for supplemental information associated with this paper is the [[https://github.com/jefferis/FruCloneClustering|github repository]] for the source code.
  * This includes an [[https://github.com/jefferis/FruCloneClustering/blob/master/src/Easy_Install_Masse.m|easy installer script]] that will [[https://github.com/jefferis/FruCloneClustering/blob/master/src/Download_Sample_Data.m|download sample data]] including:
    * [[http://flybrain.mrc-lmb.cam.ac.uk/Masse2011/FruCloneClustering/images.sel7.zip|raw confocal images]] (7 sample images, 260Mb, Biorad PIC format)
    * [[https://data.mrc-lmb.cam.ac.uk/weblinks/?id=bc6dc48b743dc5d013b1abaebd2faed2&filename=dimension_reduced_images_testset.zip|processed images for neurites]] (34 sample images, 106Mb, .mat file format)
    * [[https://data.mrc-lmb.cam.ac.uk/weblinks/?id=f2fc990265c712c49d51a18a32b39f0c&filename=reformatted_images_testset.zip|processed images for cell bodies]] (34 sample images, 475Mb, Biorad PIC format) 
    * [[http://flybrain.mrc-lmb.cam.ac.uk/Masse2011/FruCloneClustering/Registration.zip|registration data]] (53Mb)

All image data can be opened with ImageJ/[[http://fiji.sc|Fiji]]. mat files will open in Matlab or [[http://www.gnu.org/software/octave/|Octave]]. Registration data was generated with the [[http://www.nitrc.org/projects/cmtk|CMTK]] suite, which can be used for further analysis in conjunction with our [[https://github.com/jefferis/AnalysisSuite|own R code]].

Note that all raw and registered images for the [[pub:neuroanatomy:fru:|Cachero, Ostrovsky 2010 dataset]] are available on a hard drive on request to Greg Jefferis.