SNT-v5.0.0-pre-release2

🎉 This major release represents 2 years of development with significant improvements, new features, and some breaking changes.

⚠️ Important:

• 👉 Please reset SNT after updating by running File > Reset and Restart...
• 👉 This version now requires Fiji 2.16+ and Java 21+. It won't run with older Fiji versions

Analysis

• 🆕 36 new metrics including complexity indices and several extension angles (details)
• 🆕 Delineation Analyses (details)
• 🆕 Local Curvature Analysis: PCA-based analysis of neurite orientation and local curvature measurements (details)
• 🆕 Growth Analysis (details)
• 🆕 Root Angle Analysis (details)
• Sholl:
  • 🆕 Length-based and volume-based profiles (details)
  • 🆕 Angular Sholl (details)
  • ⚡ Up to 2× faster parsing of 3D images
  • ⚡ Sholl commands are finally macro recordable (details)
  • ⚡ Annotations are now placed at the center of detected components on not on the 'first seen' voxel
  • 🔧 Fix several issues including conditions affecting underestimation of equidistant neurites
• 🆕 Support for two-dimensional Histograms (details)
• 🆕 Frequency histograms can now display quartiles and Gaussian/Gaussian Mixture Models fits (example 1, example 2)
• 🆕 GUI command for Persistence Homology (details)
• 🆕 Added coefficient of variation to summary statistics (details)
• ⚡ Improved Convex Hull Analysis (details)
• ⚡ Improved Strahler Analysis with branching angles report (details)
• ⚡ Improved measurements prompt (details)

Image Analysis & Image Processing

• 🆕 Node profiler allows for cross-section profiles of paths (example, details)
• ⚡ Improved Path Profiler: Add BresenhamLine cursor and Mean+/-SD plots (details)
• ⚡ Improved Multimetric Plots (details)
• ⚡ "Convert to ROIs" can now convert branches and roots (details)

Tracing (General)

• 🆕 Machine learning: Integration with TWS and Labkit (details)
• 🆕 Bookmark Manager: New bookmark system for image locations (details)
• 🆕 Notepad Integration: Built-in notes during tracing sessions (details)
• 🆕 Option for 3D Drift correction of timelapse videos (details)
• 🆕 Option for auto-loading of CT positions (details)
• 🆕 Preliminary support for big data (details)
• ⚡ Better handling of multi-dimensional images (#211)
• ⚡ Improved interactions with Legacy 3D Viewer (details)
• ⚡ 🔧 Improvements and fixes to Match Paths Across Time... command (details)

Tracing (Automated)

• ⚡ 🔧 Improvements to soma detection and detection of perisomatic neurites (details)
• 🆕 Option for reversing paths (details)
• 🆕 Auto-connect command (details)

Tracing (Curation and Editing)

• 🆕 Proofreading Toolbar: Dedicated toolbar for proofreading operations with tagging support (details)
• 🆕 Navigation Toolbar (details)
• 🆕 Crossover detection (details)
• 🆕 Overlays can be temporarily hidden while H is pressed
• ⚡ Improved filtering options in Path manager (details)
• Path editing:
  • 🆕 Controls for adjusting radii and tagging nodes manually (details)
  • ⚡ Allow duplication of all children when duplicating a path (details)
• Path refinement:
  • 🆕 Fallback strategies for unfitted radii (details)
  • ⚡ Improved fitting criteria (#189)
  • ⚡ Improved Explore/Fit animation (details)
  • ⚡ Improved export of CSV filling details (#188, details)

Data Import/Export

• SWC I/O Improvements:
  • ⚡ Support for revised SWC specification (#203)
  • ⚡ Improved Import/Export dialogs for handling metadata (details)
  • ⚡ Faster import of large files
• TRACES Export:
  • ⚡ Allow node values to be exported to TRACES file format

Visualization

• 🆕 Create Figure... command with multi-pane (2D/3D) support (details)
• 🆕 Support for BigVolumeViewer (details)
• ⚡ Reinstated sciview functionality (details)
• Reconstruction Viewer:
  • 🆕 Implemented dedicated annotation commands (orthogonal planes, primitives, etc.) (details)
  • 🆕 Label Cartesian axes with anatomical labels (details)
  • ⚡ Fix several exceptions and issues with interactive scenes
  • ⚡ Overall adjustments for better controls and performance
• Reconstruction Plotter:
  • 🆕 All charts can now be exported as PDF (details)
  • ⚡ Viewer2D: allow fixed range in all axes (example)

Scripting & API

• 🆕 11 new template scripts and 4 new demo datasets (details)
• 🆕 Dedicated REPL (details)
• ⚡ Extended Script Recording to more commands (details)
• ⚡ Reconstruction Viewer: Allow direct retrieval of scene snapshots
• ⚡ Path anchors are now recorded during tracing when Script Recording is on
• ⚡ Improved launching from pyimagej and remote servers using X11 forwarding on Linux (JOGL-free functionality only)
• ⚡ Improved Javadocs (details)

User Interface

• ⚡ Revised and updated documentation
• ⚡ Modernized dialogs and widgets
• ⚡ Command Palette: Improved command finder with better search capabilities (details)
• ⚡ Improved file choosers with history and better integration with native file system
• ⚡ Options to load images and scripts from clipboard
• ⚡ Improved Graph editor
• ⚡ Platform-specific fixes

Core Architecture & Performance

• ⚡ Data structure overhaul: Core objects no longer use outdated arrays and are more performant and more memory efficient
• ⚡ 🔧 Better memory management: Improved resource disposal and fixed several memory leaks (#208)
• ⚡ Updated dependencies to latest versions
• ⚡ Improved test coverage

Breaking Changes

• ⚠️ Java 21 is now a minimum requirement
• ⚠️ Fiji versions older than 2.16 are no longer supported
• ⚠️ Legacy and outdated commands were removed. Use their modern counterparts instead
• ⚠️ Scripting: TreeAnalyzer deprecated. Use TreeStatistics instead
• ⚠️ Sholl directly from 3D images: Continuous sampling now uses geometric mean of voxel dimensions
• ⚠️ Order of columns may have changed in measurement tables. Make sure your macros/scripts parse column headings instead of hardwired column positions

SNT-v4.3.0-pre-release3

⚠️ This version and subsequent releases require Java 11+ ⚠️

Full Changelog: SNT-v4.3.0-pre-release2...SNT-v4.3.0-pre-release3

SNT-4.2.1

⚠️ This is the last version supported by Java 8. Newer versions will require Java 21+ ⚠️

General:

• Last version supporting Java 8

Improved:

• Handling of secondary layers:
  • Allow loading from images already open
  • Fix Rendering of MIP overlay not working for 2D images
  • Do not abort 'Sec. Layer Wizard' due to unknown image statistics
  • Allow secondary images with just one channel/frame when main image is hyperstack
  • Misc improvements and bug fixes
• Script Recording:
  • Extend recording more commands
• Command Palette:
  • Ensure listing of contextual menu commands

Full Changelog: SNT-4.2.0...SNT-4.2.1

Compiled artifact (without dependencies): SNT-4.2.0.jar

SNT-4.2.0

New:

• Weka integration (via scripting). It is now possible to train a Weka model using traced paths. Result can be loaded as a secondary tracing layer or as input for attempting automated reconstruction (#50)

Improved:

• Group analyses:
  • Scripting:
    • Added methods to GroupedTreeStatistics for two-sample t-tests and one-way ANOVA
    • Added Compare_Cell_Groups.groovy script
  • GUI (Compare Cell Groups... command):
    • Fix compartment choice being used for file filtering, and thus ignored
    • Fix single files not being considered
    • Add statistical tests to report
• Speedup loading of Shortcuts Window

Full Changelog: SNT-4.1.21...SNT-4.2.0
Compiled artifact (without dependencies): SNT-4.2.0.jar

SNT-4.1.21

Fixed:

• Several issues in Script Recorder, including #175
• Workaround for #176
• Fixed inconsistencies in font size in SNTCharts
• Misc.

Improved:

• Added 'Internode distance" mapping to TreeColorMapper
• Updated dependencies (#177, #178)

Full Changelog: SNT-4.1.20...SNT-4.1.21
Compiled artifact (without dependencies): SNT-4.1.21.jar

SNT-4.1.20

New:

• Formal Script Recorder (experimental) (Scripts -> New -> Record...)
• Notifications (example: Scripts -> Misc -> Set a Timer)

Fixed:

• Commands not visible from napari-imagej (#174)
• Misc bug fixes

Improved:

• Remove LegacyService dependency, for better pyimagej compatibility.

Changes:

• Native Open/Save dialogs can no longer be used. These have been replaced with a tweaked JFileChooser, with drag-and-drop support and other improvements.

Full Changelog: SNT-4.1.19...SNT-4.1.20
Compiled artifact (without dependencies): SNT-4.1.20.jar

SNT-4.1.19

New:

• Record option in Command Palette: Similarly to IJ's Macro Recorder, recorded calls are functional instructions that can be incorporated into scripts

Fixed:

• NDF files not being imported via drag & drop
• Truncated menu bars in M. Windows 10/11, only visible after resizing dialogs
• Misc, including #173

Improved:

• SNTCharts can now be used in headless mode
• Skeletonize... command allows paths to be exported as labels image (similar to Fill Manager's export option)

Full Changelog: SNT-4.1.18...SNT-4.1.19
Compiled artifact (without dependencies): SNT-4.1.19.jar

SNT-4.1.18

New:

• Redesigned Load Demo Dataset:
  • Use a dedicated loading class to streamline the inclusion of future demo datasets
  • Details of data (source, size, description, etc.) are included in the dialog chooser
  • All images are spatially calibrated
  • 3 additional datasets: Synaptic labeling, MouseLight dendrites, and Non-neuronal dividing cell

Fixed:

• Missing units from charts measuring disconnected path(s)

Improved:

• Opening/Running scripts through the Scripts-> menu

Full Changelog: SNT-4.1.17...SNT-4.1.18
Compiled artifact (without dependencies): SNT-4.1.18.jar

SNT-4.1.17

New:

• 'Multimetric plot' command for plotting multiple path metrics
• 'Viewer Size...' command in Reconstruction Viewer

Fixed:

• PathAnalyzer failing with single path analysis
• Erratic toggling of object visibility in Reconstruction Viewer's manager list
• Exception in ' Zoom to selection' command in Reconstruction Viewer
• Collapsed Reconstruction Viewer at startup on macOS

Improved:

• SNT initialization outside Fiji
• 'Create Annotation Graph' command

Full Changelog: SNT-4.1.16...SNT-4.1.17
Compiled artifact (without dependencies): SNT-4.1.17.jar

SNT-4.1.16

New:

• Flow plot (Sankey diagram) analyses
• New template script: Flow_and_Ferris-Wheel_Plots.groovy

Improved:

• SNTCharts:
  • Some labels/components can now be edited by double-click
  • Legends can be toggled
  • Replaced 'Lock Aspect Ratio' and 'Combine' commands with more robust alternatives
• Misc:
  • Improved handling of neurons with non-annotated nodes
  • Improved syncing of Path Manager -> Rec. Viewer
  • Improved Create Annotation Graph... command
  • Bug fixes
  • Updated dependencies

Full Changelog: SNT-4.1.15...SNT-4.1.16
Compiled artifact (without dependencies): SNT-4.1.16.jar