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{{ambox Infobox| text software = FijiThis page will hold the main documentation for the plugins distributed through the | name = Neuroanatomy update site| author = {{Person|Tiago}}| maintainer = {{Person|Tiago}}| source = {{GitHub|org=tferr|repo=hIPNAT}}| released = April 2016| status = Active| latest version = '''1.0.10 May 2017''' ({{GitHub|org=tferr|repo=hIPNAT/releases|label=Changelog}})| category = [[:Category:Plugins|Plugins]], [[User:NeuroanatomyCategory:Analysis|Neuroanatomy update siteAnalysis]], released in [http[:// April 2016Category:Neuroanatomy|Neuroanatomy]].
This is the main documentation page for the hIPNAT (''Image Processing for NeuroAnatomy and Tree-like Structures'') plugins distributed through the [[User:Neuroanatomy|Neuroanatomy update site]], released in [ April 2016]. For a list of all pages in this wiki related to Neuroanatomy have a look at [[:Category:Neuroanatomy]].
{{ambox | text =Please note that, at this time, these tools are under heavy development: some features are experimental and documentation remains incomplete. Also, some of this work has been meanwhile migrated to core-Fiji plugins, such as [[Simple_Neurite_Tracer|Simple Neurite Tracer]].
= 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 {{ListOfUpdateSites}})
# Click ''Apply changes'' and Restart ImageJ.
= List of commands =
{| class="wikitable"
|style="width:10%;vertical-align: middle;text-align:center;"|'''Name'''
|style="width:20%;vertical-align: middle;text-align:center;"|'''Menu Path'''
|style="width:70%;vertical-align: middle;text-align:center;"|'''Description'''
|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Topological Skeletons''
|- valign="top"
|Strahler classifier
|{{bc|Analyze|Skeleton|Strahler Analysis...}}
|Described in [[Strahler Analysis]].
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/skel|label=Java plugin}}.
|- valign="top"
|Summarize Skeleton
|{{bc|Analyze|Skeleton|Summarize Skeleton}}
|Bulk statistics of skeletonized images.
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/skel|label=Java plugin}}.
|- valign="top"
|Particles classifier
|{{bc|Analyze|Skeleton|Classify Particles Using Skeleton}}
|Tags particles according to skeleton features. Detects maxima on a masked image and clusters detected maxima using features of the skeletonized mask. A maxima is considered to be associated to a skeleton feature (e.g., a junction or end-point, see [[AnalyzeSkeleton]]) if the distance between its centroid and the feature is less than or equal to a cuttoff ("snap to") distance. Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.
|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 (Traces/(e)SWC)...}}
| Renders traced reconstructions ([[SNT:_.traces_File_Format|.traces]] - [[SNT]]'s format - and [ .swc] files) in ImageJ's [[3D Viewer]] or as skeletonized image stacks.
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/|label=Java plugin}}.
|Traces converter
| {{bc|Plugins|NeuroAnatomy|Convert Traces to SWC}}
| Batch conversion of [[Simple Neurite Tracer]]'s [[Simple_Neurite_Tracer:_.traces_File_Format|.traces files]] into [ SWC].
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.
|Multi-SWC renderer
| {{bc|Plugins|NeuroAnatomy|Render Multiple SWC Files}}
| Renders multiple SWC files in a single image canvas or a [[3D_Viewer|3D viewer]] universe.
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.
|Remote File renderer
| {{bc|Plugins|NeuroAnatomy|Render Remote SWC File}}
| Exemplifies how to download and access a remote (e)SWC (internet connection required).
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.
|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.
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/skel|label=Java plugin}}.
= Further information =
* A list of all pages in this wiki related to image processing in the neurosciences can be found [[:Category:Neuroanatomy|here]].