![]() idExists (): print ( "Somehow the specified id was not found", "Error" ) return a_tree = loader. isDatabaseAvailable (): print ( "Could not connect to ML database", "Error" ) return if not loader. def run (): loader = MouseLightLoader ( "AA0100" ) if not loader. Let’s get a summary of the inter-node distances for a specific mouse cortical motor neuron (ID = “AA0100” in the MouseLight database). Now you can access all the attributes and methods these classes offer. E.g., to download a neuron reconstruction from the MouseLight database and calculate summary statistics on it, you would import the MouseLightLoader and TreeStatistics classes: from scyjava import jimport MouseLightLoader = jimport ( 'sc.MouseLightLoader' ) TreeStatistics = jimport ( 'sc.' ) Then, one import the needed SNT (Java) classes. init ( 'sc.fiji:fiji', mode = 'interactive' ) Once the Python environment is properly setup, one can initialize Fiji: import imagej ij = imagej. Please refer to the complete examples for more details. Here, we will only exemplify basic functionality. The Notebooks directory in the SNT repository contains several examples at different complexity levels. This enables full integration between SNT and any library in the Python ecosystem (numpy, scipy, etc.). However, many others remain limited.ĭirect access to the SNT API from the Python programming language is made possible through the PyImageJ module. Commands for fully automated reconstructions, or generating secondary layers should work well. This includes setting filters for visibility of tags, applying Tags, or filtering paths in the Path Manager. There are two ways to start the recorder: Scripts › New › Record… or by pressing the Record button in Command Palette.Īs a rule-of-thumb, commands that are simple or do not involve prompts record flawlessly. This is particularly useful to assemble reproducible records. The goal of the recorder is twofold: 1) simplify prototyping of new scripts and 2) Log your actions during a tracing session. Note however that while the recorder captures simple commands well, it struggles to capture those that are more complex or particularly interactive. SNT features a script recorder that similarly to ImageJ’s macro recorder converts menu and button clicks into executable code. Run Scripts › Reload…, and your new script should appear in the full list of scripts found at Scripts › Full List…. Save the script in Fiji.app/scripts/ including ‘SNT’ anywhere in its file name You can choose to open an instance of Fiji’s Script Editor with preloaded boilerplate code in the scripting language of your choice or to assemble your boilerplate using the Script Recorder Go to Scripts › New… from the SNT dialog. There are a couple of ways to have your own scripts appear in SNT’s Scripts menu:Īny script saved into Fiji’s “scripts” subdirectory containing SNT in the filename (e.g., C:\Users\user\Desktop\Fiji.app\scripts\My_SNT_Script.py or /home/user/Fiji.app/scripts/My_SNT_Script.py) will be listed in Scripts menu: Did you write a useful routine? Please announce it, or submit a pull request so that it can be distributed with Fiji! Adding Scripts to SNT Your script can also be bundled with SNT, or made available through the Neuroanatomy update site. These are organized into non-rigid categories: Analysis (typically handling quantifications), Batch (Bulk processing of files), Render (visualization), Skeletons & ROIs (pixel-based analyses), Tracing (Tracing-related tasks), and Demos. There are ~50 scripts currently bundled in SNT. Script parameters are typically used for simpler routines. SNT Scripts are intentionally written in multiple languages to demonstrate flexibility, but the majority is written in Groovy and Python (Jython), for no other reason that those seem to be the most commonly used language by its developers. Typically, holding ⇧ Shift while selecting a script from a menu outside the Script Editor will open it. These can be accessed through the Plugins › NeuroAnatomy › Neuroanatomy Shortcut Window, the Scripts menu in the main dialog, or the Templates › Neuroanatomy menu in the Script Editor. This section provides an overview to the ever-growing list of SNT scripts. SNT ScriptsĪ key feature of SNT is its extensibility via scripts. The most up-to-date SNT API can be found at.
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