SNT-v4.3.0-pre-release3

⚠️ This version and subsequent releases require Java 11+ ⚠️

This is a major release with several improvements, many fixes, and some breaking changes. It is recommended to reset SNT after the update by running File -> Reset and Restart...

Release Highlights:

• General:
  • Java 11 is now a minimum requirement
  • Reinstated sciview functionality (Java21 required)
  • Improved launching from Python notebooks and remote servers using X11 forwarding on Linux (JOGL-free functionality only)
  • Extended Script Recording to more commands
• Tracing:
  • Support for revised SWC specification (#203)
  • Improved Import/Export dialogs for handling metadata (details)
  • Semi-automated:
    • Allow stats to be computed once for the full image
  • Automated:
    • Improvements to soma detection and detection of perisomatic neurites
    • Better handling of multi-dimensional images (#211)
  • Secondary Layers:
    • Integration with TWS and Labkit
    • Fix filling manager ignoring secondary layer
  • Improvements to time-lapse utilities:
    • Add demo script for automated tracing of thresholded timelapse(s)
    • Improved Match Paths Across Time... command, including fixes that did not allow proper matching of neighboring neurites
• Measurements prompt:
  • Convenience commands to define metrics and render cells being measured
  • Fix radius-related columns without spatial unit
• Path editing:
  • Auto-connect command
  • Controls for adjusting radii and tagging nodes manually
  • Command for reversing paths
  • Improved Set Active Node as Tree Root command
  • Allow duplication of all children when duplicating a path
• Path refinement:
  • Implement fallback strategies for unfitted radii and parameterize fitting criteria (#189)
  • Refine -> Correct Radii... command
  • Improved Explore/Fit animation
  • Ensure parameters persist between fits
• Fills:
  • Improved export of CSV details (#188)
• Reconstruction Viewer:
  • Fix several exceptions and issues with interactive scenes
  • Implemented dedicated annotation commands (orthogonal planes, primitives, etc.)
  • Label Cartesian axes with anatomical labels
  • Improve tagging and 'Fit to Zoom' commands
• API:
  • Lower footprint for Tree#getSkeleton2D()
  • Reconstruction Viewer: Allow snapshots to be retrieved directly
• Misc:
  • Improved Path Profiler: Add BresenhamLine cursor and Mean+/-SD plots
  • New Node profiler allows for cross-section profiles of paths (details)
  • Fix memory leaks (#208)
  • Improved Multimetric Plots
  • New Delaunay triangulation script
  • Updated dependencies
  • Updated documentation (revisions to describe newer features still required)
  • GUI improvements
  • Option to include children when duplicating Path(s)

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

SNT-v4.3.0-pre-release2

Pom: fix jogamp dependencies/updates

See https://github.com/morphonets/SNT/issues/212#issuecomment-1894761687

SNT-4.2.1

⚠️ This is the last version supported by Java 8. Newer versions will require Java 11+ ⚠️

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