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SNT: Manual

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=Startup Prompt=
[[Image:SNT-Startup-Prompt.png|right|thumb]]
Each of these SNT is initialized by running {{bc|Plugins|NeuroAnatomy|SNT...}}. All the options may in the startup prompt can be changed set once SNT is opened, but the startup prompt provides the convenience of setting the most important parameters at once.* '''Image'''/'''Image File''' Allows selection of the The image to display in the viewsbe traced/analyzed (optional). If an image is already displayed in ImageJ, it may be selected in the The drop-down menuwill list all images currently open in ImageJ. Alternatively, an image path may be specified by clicking ''Browse'' and choosing an imagefile. If no image is chosen, SNT will create an empty display canvas from the computed bounding box of the reconstruction file (if provided). If no reconstruction is provided, no placeholder image is created.* '''Reconstrucion file''' The path of the reconstruction file to importbe imported (optional). If an image SNT will automatically try to guess if there is loaded, the a reconstruction is rendered on file associated with the chosen imageby looking at all the reconstruction files (<tt>. Otherwisetraces</tt>, it is rendered in an empty display canvas<tt>. Noteworthy: If ".traces" (e)swc</tt>, or "<tt>.swc" files exist json</tt>) in the same image directory as the image selected in ''Image File'', SNT will automatically populate this field with the reconstruction file with the minimum and choosing one that more [https://en.wikipedia.org/wiki/Levenshtein_distance Levenshtein distanceclosely matches] to the image filename.* '''User interface''' Specifies which views to displayfor 3D images. The default setting provides the XY, ZY , and XZ views. Memory and screen space can be saved by choosing the ''Only XY view'' optionallows for more [[SNT:_Step-By-Step_Instructions#Accurate_Point_Placement|accurate node placement]] but requires more RAM.* '''Tracing Channel''' Specifies the image channel to trace on. If tracing on a (this option is ignored with single-channel image, leave this option as the default value (1images).
=Main Dialog=
===File===
Lists commands for I/O operations. Most are self-explanatory. Noteworthy:
[[Image:SNT-From-Open-Image-Prompt.png|right|thumb|200px|]]* {{bc|Choose Tracing Image|&nbsp;}} Specifies the image to trace onwithout having to restart SNT. To trace on an image currently open in ImageJ, use ''From Open Image...''. A prompt with the currently open images will appear, allowing selection of one. To browse for an imagefile, use ''From File...''. <div align="left"><ul> <li style="display:inline-block;"> [[Image:SNT-From-Open-Image-Prompt.png|none|thumb|200px|"From Open ImageYou should toggle the ''validate spatial calibration'' checkbox to ensure the image to be imported is compatible with the existing one..." prompt]] </li></ul></div>* {{bc|Import| Labels (AmiraMesh)...}} Allows import and rendering This option assumes you are tracing on the same spatial coordinates of AmiraMesh filesan annotated neuropil, the native file format of the for which compartments have been segmented (''labeled'') and stored in an [https://amira.zib.de/ Amira] data visualization softwarelabels file. Once loaded, SNT will report the name of the compartments in the ImageJ status bar when hovering over the image. <div align="left"><ul> <li style="display:inline-block;"> [[Image:SNT-AmiraMouseLight-MeshRemote-ExampleLoader-ImagePrompt.png|noneright|thumb|200px|AmiraMesh Fly brain]] </li></ul></div>* {{bc|Import| Remote Databases|&nbsp;}} Allows import of neuronal reconstructions from the [http://www.flycircuit.tw/ FlyCircuit], [httphttps://ml-neuronbrowser.janelia.org/ MouseLight] and [http://neuromorpho.org/ NeuroMorpho] remote databases. <div align="left"><ul> <li style="display:inline-block;"> [[Image:SNT-MouseLight-Remote-Loader-Prompt.png|none|thumb|200px|MouseLight reconstruction loader prompt]] </li></ul></div>* {{bc|Export (All Paths)|&nbsp;}} Allows export of all traced paths in the [http[SNT://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html _FAQ#swc|SWC]] file format, a widely used standard the most common format for representing neuronal reconstructions which is supported by most annotation and visualization software. Note that you can also export subsets of paths using the [[#Path Manager|Path Manager]]. Additionally, useful numeric properties of paths can be stored in a CSV file by choosing the ''CSV Properties...'' export option.
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