SNT-4.0.10

This is a maintenance release that has not been uploaded to the Neuroanatomy update site.

SNT-4.0.9

New:

• Combine Plots Into Montage... command: Combines isolated charts (plots, histograms, etc.) into a multi-panel canvas
• Script for convex hull bulk analyses (#88)

Improved:

• Previous 'single-cell' commands (Convex Hull, Sholl, Strahler, ...) can now be run on multiple cells
• Updated dependencies

Fixed:

• Selection of multiple items in Rec. Viewer not working as expected in certain cases
• Detection of sub-arbors ('axon', 'dendrites') within a reconstruction not working as expected in certain edge cases
• Rendering of some ill-tagged SWC files in Reconstruction Viewer/sciview (#81)
• Minor issues

Full Changelog: SNT-4.0.8...SNT-4.0.9
Compiled artifact (without dependencies): SNT-4.0.9.jar

SNT-4.0.8

Improvements:

• Option to perform Sholl analysis from soma-tagged paths that are not at the root of the reconstruction (details)
• New template script: Templates→ Neuroanatomy→ Analysis→ Sholl Convex Hull As Center (details)

Fixed:

• Issue affecting the subprocess in Jython (details)

Full Changelog: SNT-4.0.7...SNT-4.0.8
Compiled artifact (without dependencies): SNT-4.0.8.jar

SNT-4.0.7

Fixed regression #81 introduced in v4.0.6.

Full Changelog: SNT-4.0.6...SNT-4.0.7
Compiled artifact (without dependencies): SNT-4.0.7.jar

SNT-4.0.6

Improvements:

• Refined Path rendering (node color coding, transparency, etc.). Diameters are now displayed in side views
• Refined Path tagging operations
• Better organization of menu commands. Majority of commands now features tooltip hints
• New script for modifying CT positions of Paths when tracing multichannel or timelase images

Fixed:

• Reinstated sciview support (#53)
• "Show nodes within # Z-slices" not editable after changing tracing image
• Reconstruction Plotter extremely slow when rendering large (>1K) color-coded structures
• Outdated documentation URLs
• Misc issues

Full Changelog: SNT-4.0.5...SNT-4.0.6
Compiled artifact (without dependencies): SNT-4.0.6.jar

SNT-4.0.5

• Fixed:
  • Paths not partitioned by type on SWC import (details)
  • IJ1 GenericDialog's not displaying when setting customizing SNT's Look and Feel on MacOS (details)
  • 'Select nearest path at cursor' failing to recognize single paths
  • Edit mode auto-disabling after graph-based edits
  • Several issues with Reconstruction Plotter, namely: Monchrome snapshots; Color ramp legend not updating after toggling dark mode; Grid lines being reset when refreshing/updating canvas
  • 'Ghosting' effect when rotating large meshes in Reconstruction Viewer
  • Regression introduced in v4.0.4 in which animations in Reconstruction Viewer could no longer be disabled with single mouse click
  • Other minor issues
• Improvements:
  • New template script exemplifying how to script Reconstruction Viewer in headless mode (details)
  • Option in Reconstruction Viewer to reveal snapshot directory in File Manager

Full Changelog: SNT-4.0.4...SNT-4.0.5.
Compiled artifact (without dependencies): SNT-4.0.5.jar

SNT-4.0.4

• Reconstruction Viewer:
  • New: Support for off-screen (headless) canvases, useful for obtaining programmatic snapshots of scenes without displaying them
  • New: Support for EmulGL (CPU rendering), useful for machines without GPU, or installations with problematic JOGL installs.
  • New: Support for Allen CCFv3 (mouse atlas)
  • Improved: Consistency of preset ("Ctrl+click") views
  • Fixed: #69
• Tracing:
  • New: Subvolume statistics are now enabled by default (details)
  • Improved: Path Fitting performance (up to 30x faster!) (#72)
• Analysis:
  • New: timelapse_segmentation notebook (details)
  • Improved: MouseLight reconstructions are now handled in CCFv3
  • Fixed: Topological artifact when scaling/translating a tree

Full Changelog: SNT-4.0.3...SNT-4.0.4
Compiled artifact (without dependencies): SNT-4.0.4.jar

SNT-4.0.3

Maintenance Release:

• Fixed: Export of Paths' CSV Properties
• Misc: Minor GUI improvements
• Misc: Updated dependencies

Full Changelog: SNT-4.0.2...SNT-4.0.3
Compiled artifact (without dependencies): SNT-4.0.3.jar

SNT-4.0.2

• New: Fill Demo script (details)
• New: Ability to export fills as label image (example)
• New: 2D and 3D Convex Hull analyses
• Improved: Several bug fixes and improvements, including #64, #65
• Misc:
  • Javadocs are now accessible through https://javadoc.scijava.org/
  • hIPNAT scripts and commands have been incorporated into SNT. This fixes a couple of 'ClassNotFound' exceptions, and improves the organization of the Neuroanatomy update site.

Full Changelog: SNT-4.0.1...SNT-4.0.2

Compiled artifact (without dependencies): SNT-4.0.2.jar

SNT-4.0.1

• New: Improvements to Path Profiler: (arbitrary widths, customizable neighborhoods (disc, circle, sphere, etc.). See #62 for details
• New: Path Straighten command
• Improvements: Misc bug fixes and improvements, including #63, #61, #60, #57

Compiled artifact (without dependencies): SNT-4.0.1.jar