https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/ 2026-05-14T19:08:40+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 2013-12-10T11:59:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=software:amira:adding_a_scale_bar&rev=1386676785&do=diff To use a scale bar sensibly in Amira, you need to * Switch to orthographic projection (ie where the cube looks like a cube and the scene does not have a vanishing point) * Add a 2D measurement * try to get it as horizontal as possible but you can fix this up later 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=software:amira:crashes&rev=1386676785&do=diff Crash from loading a script object from recent files Process: amiramain [5985] Path: /Applications/Amira-5.3.3/bin/arch-MacX-Optimize/amiramain Identifier: com.visageimaging.amira533-20101217-000004 Version: 5.3.3 (???) Code Type: X86 (Native) Parent Process: launchd [1536] Interval Since Last Report: 70 sec Crashes Since Last Report: 1 Per-App Interval Since Last Report: 52 sec Per-App Crashes Since Last Report: 1 Date/Time: … 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=software:amira:developer&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. ~/dev/amiradev this is $AMIRA_LOCAL * replace $AMIRA_LOCAL/src with checkout of felix's svn * Install binary qt 4.3.4 (qt-mac-opensource-4.3.4.dmg from trolltech/mirrors) 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=software:amira:grouping_surface_regions&rev=1386676785&do=diff Grouping To make a grouping in a Surface file: * Set up a groupings panel by creating a SurfaceView and then selecting Groupings from the top left (or right clicking on the surface view object) * Manipulate your materials such that the precise set of features that you want the group to recall is displayed - this 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=software:amira:hxskeletonize&rev=1386676785&do=diff Official information still seems to be on Felix's Berlin homepage although this is quite old now. Installation * I have most recently compiled this for Amira 5.3.2 on MacOS X 10.6 * I normally distribute this as a zip archive containing two sets of files in nested folders that match the main Amira folders: text/html 2015-12-18T13:37:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=software:amira:read_nrrd_files&rev=1450445828&do=diff Intro Most of our image processing is based around NRRD files as an intermediate image format. CMTK, ImageJ/Fiji and R can read/write them. But commercial Amira cannot by default. ZIB Amira can. I have written a small plugin for Amira that lets it read and write nrrd files. text/html 2018-02-13T12:31:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=software:amira:stackviewer&rev=1518525103&do=diff StackViewer.hx is an Amira script that allows you to quickly review many 3D stacks e.g. in Amiramesh or NRRD format. It can also show a template brain for comparison. It is a little simpler than the ResultViewer.hx script which is targeted specifically at reviewing and making affine registrations. 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=software:amira:start&rev=1386676785&do=diff Amira is a 3d visualisation software. It has its quirks and is far from free, but provides good all round visualisation, mixing of fast volume rendering and surface rendered neurons and access to Felix Evers' semi-automated tracing plugin. * Developer * Zib Amira * Admin * Grouping Surface Regions * Tracing neurons with hxskeletonize * Crashes * Read NRRD files * Using ShowClones to switch between and colorize volume renderings of different stacks e.g. clones or any other maske… text/html 2017-12-17T09:19:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=software:amira:using_resultviewer&rev=1513502384&do=diff Introduction I have written a tcl script, ResultViewer.hx, based on work from Steffen Prohaska that allows * visualisation in Amira of affine registered brains compared with a template * selection of what kind of affine (9dof, ght etc) * selection of a template brain (FC6475, FCWB) 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=software:amira:using_showclones&rev=1386676785&do=diff showClones.scro is an Amira TCL script that lets you quickly change between different volume renderings. But to have a lot of volume renderings active, the data must be small. Downsampling and cropping to just the data of interest are important for this.