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Releases: morphonets/SNT

SNT-v4.3.0-pre-release3

08 Mar 19:15
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Pre-release

⚠️ 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

08 Jan 10:36
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Pre-release
Pom: fix jogamp dependencies/updates

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

SNT-4.2.1

18 Jan 03:16
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DOI

⚠️ 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

27 Jun 01:40
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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

23 Jun 01:43
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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

11 Jun 13:18
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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

05 Jun 11:04
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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

30 May 11:44
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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

12 May 12:48
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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

04 May 15:18
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New:

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