SNT-3.2.4

Tracing:

• New: Commands for counting spines/varicosities/terminals and related analyses (details)
• New: Allow paths to be measured individually (details)
• Improved: More responsive PathManager, specially with large collections of Paths

General:

• Improved Grouped- and Multi- TreeStatistics
• Improved PathManager tagging
• Misc improvements and bug-fixes

Compiled artifact (without dependencies): SNT-3.2.4.jar

SNT-3.2.3

General:

• Improved: Plots and histograms now have a scaling and a dark theme option
• Improved: Histograms from GroupedTreeStatistics commands (e.g., 'Import and Compare Groups...') are now normalized
• Improved: misc. issues solved

Tracing:

• New: Added 3D & 4D examples to File > Choose Tracing Image > From Demo...
• New: Added the "Select Paths by ROI" command (option in canva's contextual menu)
• New: Added a preference for adopting 2D display canvases at all times

Sholl:

• Improved: Streamlined and fixed several issues with the Sholl Analysis (from Image)... interactive prompt
• New: Implemented "Normalized integrated intensity" and "Cumulative distribution" plots (details)
• New: Added Sholl Rasterize Shells script (details)

Scripting:

• Allow traces to be loaded from remote servers

Compiled artifact (without dependencies): SNT-3.2.3.jar

SNT-3.2.2

General :

• Improved: More 'color mapping' metrics
• Improved: Streamlined menus and commands in "Neuroanatomy Shortcuts Window"
• Improved: Simplified the analysis of untagged reconstructions
• Improved: Simplified "Compare Groups" command
• Fixed: Addressed error-when-using-sholl-parsing-in-snt
• Fixed: Addressed macro-recording-of-sholl-analysis-plugin-failing
• Fixed: Misc. issues

Noteworthy:

• sciview interface is currently broken. See #51 for updates

Compiled artifact (without dependencies): SNT-3.2.2.jar

SNT-3.2.0

General :

• New: Ability to open the Neuroanatomy Shortcuts Window command from the main ImageJ toolbar (look for the Neuroanatomy Shortcuts in the ">>" More Tools drop-down menu)
• New: Options to customize the look and feel of SNT, including dark themes and scalable HiDPI themes (particularly useful in linux where scaling of GUI components remains problematic)
• Improved: The Plugins>Neuroanatomy> submenu is now properly sorted in the Fiji's Plugins> menu hierarchy
• Improved: Faster startup times
• Improved: Miscellaneous bug fixes

Reconstruction Viewer:

• New: Added a 'Duplicate scene' command
• Improved: More responsive imports via drag & drop

Tracing:

• Fixed: Option for no. of thread defaulting to 1 after resetting preferences
• Fixed: Channel scrollbar not being displayed when loading a 2D (converted-)RGB image at startup

Noteworthy:

• sciview interface is currently broken. See #51 for updates

Compiled artifact (without dependencies): SNT-3.2.0.jar

SNT-3.1.118

Reconstruction Viewer:

• Fixed: Severe bug that could crash the program when loading a mesh on an non-empty scene
• Improved: Scene rebuilds
• Improved: Loading of meshed from CCF Navigator and via drap & drop

Analysis:

• Improved: DirectedWeightedGraph <>Tree conversion
• Improved: DirectedWeightedGraph API
• Improved: Faster shortest path calculation

Other:

• Improved: regression tests
• Fixed: minor issues
  Noteworthy:
• sciview interface is currently broken. See #51 for updates

Compiled artifact (without dependencies): SNT-3.1.118.jar

SNT-3.1.117

Tracing:

• Fixed: Auto-tracing failing when using a list of points as input

Reconstruction Viewer:

• Fixed: display canvases being assembled when importing reconstructions from remote databases
• Fixed: Inaccurate progress bar when import by drag & drop included files containing multiple reconstructions
• Fixed: some options in import commands not remembered across starts
• Improved: Consistency of import prompts
• Improved: Added ShiftR as shortcut for validating/reloading scene
• Improved: Streamlined deletion of scene objects
• Improved: Progress bar now reports on time-consuming operations
• Improved: Added an option to add a text annotation to a scene

Other:

• Fixed: Status bar in Path Manager/RV controls displaying inaccurate object count
• Improved: In the "Compare Groups" command, groups can now be specified in any order
• "Demo" scripts are now listed in the Scripts menu (before, such scripts were only accessible in Script Editor's 'Templates' menu)
• New longest shortest-path algorithm in DirectedWeightedGraph
• Updated dependencies

Noteworthy:

• sciview interface is currently broken. See #51 for updates

Compiled artifact (without dependencies): SNT-3.1.117.jar

SNT-3.1.116

Tracing:

• Custom tags and colors are no longer lost when splitting a Path/Tree

Reconstruction Viewer:

• Loading of reconstructions improved:
  • Bulk import by drag and drop is now faster
  • "Import Directory" command now allows for filename filtering
  • By default, axonal and dendritic arbors of an imported Tree will have their dendrites and axons split into separated objects (toggleable option)
  • Improved loading of multiple cells saved in a single file
  • Scripting: Added convenience methods to facilitate imports:

 addTrees(File[] files, String color)
 isSplitDendritesFromAxons()
 setSplitDendritesFromAxons(boolean split)

• Fixed an issue in which "Dark mode" toggling could fail with incomplete reconstructions

Misc:

• Updated Template scripts so that more demos can run without any user input

Compiled artifact (without dependencies): SNT-3.1.116.jar

SNT-3.1.115

(Intermediate release)

Compiled artifact (without dependencies): SNT-3.1.115.jar

SNT-3.1.114

Tracing:

• Bugfix: A* search failing on 16- and 32-bit images because min/max of image were not being retrieved properly (reported here)
• Worked around an edge case in which loading a large 2D binary image in the startup prompt would fail

Compiled artifact (without dependencies): SNT-3.1.114.jar

SNT-3.1.113

Tracing:

• Loading of large reconstructions into Path Manager is significantly faster now
• Improved Editing of paths
  • Splitting operations are now supported
  • Fix ghost connections at canvas origin upon node/path deletion (reported here)
  • Deletion of junction nodes is no longer allowed. Use 'Split' instead

Misc:

• Improved detection of paired files (image/reconstruction) in startup prompt
• Improved behavior of display canvas(es)

Scripting:

• Fixed #47
• Migrated Javadocs to javadoc.scijava.org
• Modernized python notebooks
• Simplified initialization of Reconstruction Viewer from python:

Viewer3D = jimport('sc.fiji.snt.viewer.Viewer3D')
viewer_3d = Viewer3D(False)  ## Non-interactive viewer (without RV controls)
viewer_3d = Viewer3D(True)   ## interactive viewer (with RV controls)

Compiled artifact (without dependencies): SNT-3.1.113.jar