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  2. Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/feed.php
    31 May 2024: odd_on_acq4&rev=1639657677&do=diff acq4 acquisition software for the new sensapex system provides a new challenge for running the XOP.
  3. NBLAST

    flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/
    7 Jun 2022: Such data demand new computational tools to search and organize neurons.
  4. start - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/
    Jefferis Lab. This is the informal website for Greg Jefferis' Lab based in the Division of Neurobiology of the MRC Laboratory of Molecular Biology where Greg has an official page. We have strong links with the Department of Zoology of the University
  5. Finding the mAL Neurons

    flybrain.mrc-lmb.cam.ac.uk/si/nblast/knitr/mAL.html
    3 Apr 2015: Let’s cluster those and see what we have. hcmal=hclustfc(mals). ## The "ward" method has been renamed to "ward.D"; note new "ward.D2". ... The "ward" method has been renamed to "ward.D"; note new "ward.D2".
  6. Jefferis Lab DokuWiki software:amira

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/feed.php?mode=list&ns=software:amira
    31 May 2024: rev=1386676785&do=diff Setting up AmiraDev to compile Felix's source hxskeletonize/hxgrapheditor Amira 5.2.2 Use Wizard to make a new amiradev folder e.g.
  7. NBLAST_search

    flybrain.mrc-lmb.cam.ac.uk/si/nblast/knitr/NBLAST_search.html
    3 Apr 2015: R/R18C12_voxdims.am", format='hxlineset', F=T) #resave with new name #R18C12=read.neuron(f="/GD/LMBD/Papers/2012NBlast/R/R18C12_voxdims.am")
  8. Jefferis Lab DokuWiki warping_manual

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/feed.php?mode=list&ns=warping_manual
    31 May 2024: Whenever you start a new job it saves a. command file in this directory. ... diff There are number of things that are worth optimising when first starting to register a new kind of image.
  9. warping_manual:start - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:start
    Original gui to use CMTK on a Mac. Also new Fiji based cross-platform.
  10. software:amira:developer - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=software:amira:developer
    Setting up AmiraDev to compile Felix's source hxskeletonize/hxgrapheditor. Amira 5.2.2. Use Wizard to make a new amiradev folder e.g.
  11. pub:neuroanatomy:fru:faqs - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:faqs
    machine). PC: eSATA for excellent performance on new PCs. USB2.0 slow, but very cheap and works on all machines.
  12. pub:neuroanatomy:fru:template_brains - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=pub:neuroanatomy:fru:template_brains
    The output file of the avg_adm tool was used as the new template to which each image was registered. ... The avg_adm command was again called and its output was the new Intersex template.
  13. software:amira:grouping_surface_regions - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=software:amira:grouping_surface_regions
    On the Groupings panel select New Group and give it a name. ... The order is harder to change - one must redefine the groups from start to finish by selecting the group, creating a new group from it and then deleting the old one.
  14. flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?do=export_raw&id=warp…

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?do=export_raw&id=warping_manual:plotting_3d_objects_in_r
  15. NBLAST

    flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/rss.xml
    13 Jul 2019: layout: post category : pages tags : [how-to, jekyll] ---. contents. </code></pre> <p>Three hyphens on a new line start the Front-Matter block and three hyphens on a new line end
  16. software:amira:hxskeletonize - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=software:amira:hxskeletonize
    Top Tips. You may need to move the tracing toolbar to a new location (e.g.
  17. warping_manual:registration_gui - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui
    Hit OK - this creates a small script in /yourregistrationfolder/commands. Navigate to the /yourregistrationfolder/commands folder, you will find a new file called munger_<todays date>_<time file created>.command, double
  18. flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?do=export_raw&id=star…

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?do=export_raw&id=start
    ERC Consolidator Grant NeuroNex2 (see https://neuronex.org/news/13) Wellcome Trust (Collaborative Award, see http://www.zoo.cam.ac.uk/research/groups/connectomics) Wellcome Trust ([[http://virtualflybrain.org|VFB]] - Biomedical
  19. flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?do=export_raw&id=soft…

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?do=export_raw&id=software:amira:developer
    Setting up AmiraDev to compile Felix's source hxskeletonize/hxgrapheditor ====== Amira 5.2.2 ====== Use Wizard to make a new amiradev folder e.g.
  20. warping_manual:custom_command_lines_for_munger.pl - Jefferis Lab…

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:custom_command_lines_for_munger.pl
    Whenever you start a new job it saves a. command file in this directory. ... You can open these in a text editor to slightly modify the commands, or double click them to re-run the command (a new Terminal window will open.
  21. warping_manual:plotting_3d_objects_in_r - Jefferis Lab DokuWiki

    flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:plotting_3d_objects_in_r
    This is clearly a bit naff. So in the past what I did was manually multiply all y and z coordinates by -1 to end up with a new object that

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