Skip to content, Skip to search



2,578 bytes added, 16:30, 3 June 2016
Add list of commands. Restructured text
{{ambox | text =
This page will hold is the main documentation page for the plugins distributed through the [[User:Neuroanatomy|Neuroanatomy update site]], released in [ April 2016].}}[[Category:Neuroanatomy]]   = Installation =The requirements to run the Neuroanatomy suite of plugins are twofold: i) [[Fiji]] (i.e., an ImageJ installation subscribed to the Fiji update site) and ii) Java 8 (as part of an active effort to [[2015-12-22_-_The_road_to_Java_8|modernize ImageJ]]). If you are running an older version of Java, you can either i) [[Fiji/Downloads|Download the latest Fiji release]] (newer releases come pre-bundled with Java 8); or ii) If you have downloaded Fiji while ago and want to keep your existing installation, you will have to download Java 8 and make your [[Troubleshooting#Checking_the_Java_version|Fiji installation aware of it]]. '''Subscribing to the Neuroanatomy update site:'''# Run [[Update_Sites|{{bc|Help|Update...}}]]# Click ''Manage update sites''# Select the ''Neuroanatomy'' checkbox (see also [[List of update sites]])# Click ''Apply changes'' and Restart ImageJ. = List of commands ={| class="wikitable"|style="vertical-align: middle;text-align:center;"|'''Name'''|style="vertical-align: middle;text-align:center;"|'''Menu Path'''|style="vertical-align: middle;text-align:center;"|'''Description'''|-|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Topographic Skeletons''|- valign="top"|Strahler classifier|{{bc|Analyze|Skeleton|Strahler Analysis...}}|Described in [[Strahler Analysis]]|- valign="top"|Summarize Skeleton|{{bc|Analyze|Skeleton|Summarize Skeleton}}|Bulk statistics of skeletonized images|- valign="top"|Particles classifier|{{bc|Analyze|Skeleton|Classify Particles Using Skeleton}}|Tags segmented particles according to skeleton features|-|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Import/Export''|- valign="top"|Tracings Importer| {{bc|File|Import|Tracings (SWC/Traces)...}}| Renders traced reconstructions ( .traces - [[Simple Neurite Tracer]]'s format - and .swc files) in ImageJ's [[3D Viewer]] or as skeletonized image stacks|-|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Utilities''|- valign="top"|Fractal Trees| {{bc|File|Open Samples|Fractal Tree}}| Synthetic images (L-System Trees) useful for debugging, testing or prototyping|}  = Further information =* A list of all pages in this wiki related to Image Processing in the Neurosciences can be found [[:Category:Neuroanatomy|here]].* The Neuroanatomy toolbox is maintained by [[User:Tiago|Tiago Ferreira]]* The source code is available on [ GitHub] 
See also: [[:Category:Neuroanatomy]].