SNT-4.0.0

Major rewrite of core functions to support ImgLib2 data structures, with many improvements to tracing algorithms

Highlights (non-exhaustive):

• Tracing:
  • Faster (up to 30x!) path finding searches (see #59 for some benchmarks)
  • Ability to mix and match cost functions, heuristics, and search strategies
  • Added a new probabilistic cost function
  • Imagery is now represented and handled internally using imglib2 data structures, providing the ability to perform searches over arbitrary RandomAccessibleIntervals. This sets the stage for future integration with BigDataViewer and sciview
  • Improved multi-scale enhancement filters (see #59 for details)
  • Support for real-time local filtering of the image during A*-search
  • Adaptive, local image statistics computations used by searches (optional), enables tracing over large volumes where computing the entire image statistics is prohibitive
  • Preliminary support for tracing and filling of arbitrarily large image volumes via scripting

Misc:

• Various UI improvements, including the new computation settings panel and improved Fill Manager interface
• Several breaking API changes
• Several bug fixes

Full Changelog: 3.1.108...SNT-4.0.0

SNT-3.2.14

Fixed an issue in which files with paths connected via 'end-joins' would fail to import (details)

SNT-3.2.13

Several improvements to Path Editing operations (details):

• New: Allow editable nodes to be 'locked'
• New: Allow paths to be concatenated
• New: Out-of-focus nodes are no longer automatically hidden when switching to Edit Mode. Use the respective option in the main tab to toggle this filtering option at will (shortcut key: 2 )
• Fixed: Paths are no longer renamed when re-arranging relationships between paths
• Fixed: Several issues with "Merge primary Paths in Shared Root". The operation is now undoable
• Fixed: An issue in which paths could not be merged due to a 'loop detected' error
• Fixed: Several issues that could cause path's hierarchy to be modified when performing certain operations (details)
• Fixed: Misc inconsistencies

Misc:

• New: Added more options for selection of 'child paths' in Path Manger
• Fixed: Sholl Merge Grouped Profiles uses bin centers (details)
• Fixed: Mirroring of trees not working as expected
• Fixed: ConcurrentModificationException with certain selections in Path Manager
• Breaking Change: Removal of 'end-joining' operations. Historically, Simple Neurite Tracer allowed paths to be joined at either a 'starting node' or an 'ending node'. This made the code way more complex than it needs to be. In this release, we decided to remove this feature and allow only paths to be joined at starting nodes. Rationale:
  • It increases the complexity of code and slows things down. Its removal makes handling of paths noticeably faster!
  • (Arguably) It is no longer needed since the addition of path editing controls (that did not exist in Simple Neurite Tracer)
  • This option has not been accessible from the GUI for several years now
  • It is very hard to understand what end-joining is when analyzing complete reconstructions
  • TRACES files affected by this should still be import as expected.

SNT-3.2.12

Interim release

SNT-3.2.11

• Temporary workaround for File -> Save Tables & Analysis Plots... failing with SciJava tables (details)
• Fix for "Sholl: Ignore somatic segments" w/ discontinuous step size (details)
• Generalized Sholl Merge Grouped Profiles script so that it can be used to merge any type of profiles (details)
• Other bugfixes and improvements

Compiled artifact (without dependencies): SNT-3.2.11.jar

SNT-3.2.10

• New: File -> Save Tables & Analysis Plots... (also in Reconstruction Viewer's Analyze & Measure menu) saves all analyses file(s) in one go
• Adjusted the dimensions of main dialog (so that it is not displayed with exaggerated dimensions on MacOS)
• Bug fixes and misc improvements

Compiled artifact (without dependencies): SNT-3.2.10.jar

SNT-3.2.9

• Tracing: Added option to completely hide out-of-plane segments (details)
• Reconstruction Viewer: Added option to zoom scene to selected object(s)
• Bug fixes and misc improvements

Compiled artifact (without dependencies): SNT-3.2.9.jar

SNT-3.2.8

• Tracing:
  • Bug fixes and improvements in GUI
• Sholl Analysis:
  • New option to ignore somatic segments (details)
  • Improved saving of files in bulk analyses
• Reconstruction Viewer:
  • Added Command Finder

Compiled artifact (without dependencies): SNT-3.2.8.jar

SNT-3.2.7

• New: Added "SNTCommandFinder", a remake of IJ's Command Finder for SNT's GUI. Look for the search icon on the end of SNT dialogs
• Fixed: "Path nodes rendering scale" not working Details
• Fixed: Take Snapshot script not respecting "Path nodes rendering scale" setting
• Fixed: Issue with Reconstruction From Segmented Image script Details
• Misc improvements and bug-fixes

Compiled artifact (without dependencies): SNT-3.2.7.jar

SNT-3.2.5

Sholl Analysis:

• Improved: Do not override cells on re-analysis, which facilitates simultaneous analysis of multiple cells (details)
• Improved: Fixed several inconsistencies in dialog prompts
• New: Option to include/exclude zero-count entries

General:

• Misc improvements and bug-fixes

Compiled artifact (without dependencies): SNT-3.2.5.jar