https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/ 2026-05-14T20:09:58+00:00 https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/ https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/lib/tpl/monobook/images/favicon.ico text/html 2016-10-05T11:36:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:clone_correspondences&rev=1475667419&do=diff This table shows likely correspondences between the various nomenclatures assigned to fruitless positive neurons. It is incomplete and subject to change, but overall should be correct. Note that not all correspondences are one-to-one, as different labeling techniques (MARCM, fruFLP, PA-GFP, fru vs dsx) yield different expression patterns. text/html 2017-05-15T14:05:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:data&rev=1494857111&do=diff In additional to supplemental data available via the Current Biology website, we are providing two large collections of image data: * 3Gb of key image data (available on the Web) * >1Tb of comprehensive image data including all raw and processed confocal stacks (available by external hard drive) text/html 2013-12-10T11:59:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:faqs&rev=1386676785&do=diff FAQs * I am having trouble opening the images. * All images can be opened by the stock version of Fiji. You can then convert to pretty much any format you want. See also Software page. * In the Successfully Registered image, some of the images have three channels. I am wondering what is the '03' stained for? text/html 2013-12-10T11:59:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:image_processing_pipeline&rev=1386676785&do=diff Image Processing Overview Every image in our dataset was registered against a template brain to bring them into a standard coordinate system resulting in a reformatted image. The reformatted images were then extracted using different binary masks according to which fru+ MARCM clones were present. So each image could potentially result in e.g. 10 different text/html 2013-12-10T11:59:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:registration_parameters&rev=1386676785&do=diff We used the following command lines to run munger.pl for both brains and VNCs: munger.pl -b /path/to/cmtk/binaries -vawr 010203 -T 4 -X 26 -C 8 -G 80 -R 4 \ -A '--accuracy 0.4' -W '--accuracy 0.4' -s "refbrain/IS2.PIC" "images" # identical except for reference image munger.pl -b /path/to/cmtk/binaries -awr 010203 -T 4 -X 26 -C 8 -G 80 -R 4 \ -A '--accuracy 0.4' -W '--accuracy 0.4' -s "refbrain/VNCIS1.PIC" "images" text/html 2013-12-10T11:59:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:software&rev=1386676785&do=diff * Registration software * Fully open source cross-platform CMTK software by Torsten Rohlfing and collaborators. * Simple GUI wrapper for CMTK (MacOS X only). * Source code for Neuroanatomy Analysis Suite for R. Available from: * <http://flybrain.stanford.edu/R> * as a git repository * Our ImageJ plugins are now bundled with text/html 2013-12-10T11:59:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:start&rev=1386676785&do=diff These pages describe the supplemental data and software available online or via >=1.5Tb external hard drive to accompany: Cachero S., Ostrovsky A.D., Yu J.Y., Dickson B.J., and Jefferis G.S.X.E. (2010). Sexual Dimorphism in the Fly Brain. Current Biology doi:10.1016/j.cub.2010.07.045 The article is freely available as open access ( text/html 2013-12-10T11:59:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:template_brains&rev=1386676785&do=diff Standard Template Generation * Templates are generated from a selection of 15-30 nc82 stained images that are well stained and sit flat on the slide. Each image was taken from the same sex to generate sex specific templates. * One brain is chosen as the initial seed. This brain was selected because it was felt it was best stained and sat most symmetrically.