MagellanMapper v1.6 beta 4

Highlights in v1.6 pre-releases

• Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
• Available as binary wheel to install without requiring the source code
• Faster, lighter installation with fewer required dependency packages
• Extends suppor to Python 3.11 and defaults to Python 3.9
• Simpler entry point to launch MagellanMapper: mm
• Supports ITK-Elastix for image registration
• Atlases can be downloaded directly through BrainGlobe (see the new "Atlases" panel)
• Atlas regions can be searched (see "Atlases > Region")
• Atlas Editor planes can be reordered or turned off
• Detection channels can be selected independently of the loaded image to overlay prior detections or compare channels (see "Detect > Chl")
• Images can be viewed as RGB (see "ROI > Channels") or merged channels
• Jupyter Notebook tutorial for running common tasks
• Fixed installation on Apple Silicon (Mac M-chip) platforms

Major changes since beta 3

• Fixed installation on Apple Silicon (Mac M-chip) platforms (#634)
• Select colormaps for each channel (#574)
• Fixed image adjustment controls
  • Fixed synchronization between images and adjustment controls (#576)
  • Fixed intensity sliders to cover the full range (#572, #576, #606, #613)
  • Fixed intensity range of "filtered" ROI and overview images (#613)

See the full release notes draft here for more details.

All Changes

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• Bump default Python version to v3.9 by @yoda-vid in #559
• Bump imageio from 2.31.3 to 2.31.4 in /envs by @dependabot in #560
• Bump tifffile from 2023.9.18 to 2023.9.26 in /envs by @dependabot in #561
• Bump scipy from 1.11.2 to 1.11.3 in /envs by @dependabot in #562
• Fix ReadTheDocs for Python 3.9 by @yoda-vid in #563
• Bump cycler from 0.11.0 to 0.12.0 in /envs by @dependabot in #564
• Bump imageio from 2.31.4 to 2.31.5 in /envs by @dependabot in #565
• Bump fonttools from 4.42.1 to 4.43.0 in /envs by @dependabot in #566
• Bump charset-normalizer from 3.2.0 to 3.3.0 in /envs by @dependabot in #568
• Bump urllib3 from 2.0.5 to 2.0.6 in /envs by @dependabot in #569
• Bump rich from 13.5.3 to 13.6.0 in /envs by @dependabot in #570
• Bump packaging from 23.1 to 23.2 in /envs by @dependabot in #571
• Bump scikit-image from 0.21.0 to 0.22.0 in /envs by @dependabot in #573
• Extend image adjustment sliders to use full intensity range by @yoda-vid in #572
• Store the last opened image via the GUI in preferences by @yoda-vid in #575
• Select colormaps in the GUI by @yoda-vid in #574
• Fix restoring intensity when showing a multi-channel image with deselected channels by @yoda-vid in #576
• Bump cycler from 0.12.0 to 0.12.1 in /envs by @dependabot in #577
• Bump fonttools from 4.43.0 to 4.43.1 in /envs by @dependabot in #578
• Bump traits from 6.4.2 to 6.4.3 in /envs by @dependabot in #579
• Bump urllib3 from 2.0.6 to 2.0.7 in /envs by @dependabot in #581
• Bump pyqt5-sip from 12.12.2 to 12.13.0 in /envs by @dependabot in #582
• Bump imageio from 2.31.5 to 2.31.6 in /envs by @dependabot in #583
• Bump charset-normalizer from 3.3.0 to 3.3.1 in /envs by @dependabot in #584
• Bump numpy from 1.26.0 to 1.26.1 in /envs by @dependabot in #586
• Bump networkx from 3.1 to 3.2 in /envs by @dependabot in #587
• Bump pandas from 2.1.1 to 2.1.2 in /envs by @dependabot in #588
• Bump networkx from 3.2 to 3.2.1 in /envs by @dependabot in #589
• Bump pyqt5 from 5.15.9 to 5.15.10 in /envs by @dependabot in #590
• Bump charset-normalizer from 3.3.1 to 3.3.2 in /envs by @dependabot in #591
• Bump contourpy from 1.1.1 to 1.2.0 in /envs by @dependabot in #593
• Bump matplotlib from 3.8.0 to 3.8.1 in /envs by @dependabot in #594
• Bump importlib-resources from 6.1.0 to 6.1.1 in /envs by @dependabot in #596
• Bump imageio from 2.31.6 to 2.32.0 in /envs by @dependabot in #597
• Bump fonttools from 4.43.1 to 4.44.3 in /envs by @dependabot in #598
• Fix making density images with ITK by @yoda-vid in #599
• Support generating regional heat maps from the volume metrics output by @yoda-vid in #600
• Remove verify_tol_factor from identical block settings check by @yoda-vid in #603
• Exclude negative intensities by default in image sliders by @yoda-vid in #606
• Workaround Matplotlib error when turning off alpha blending by @yoda-vid in #607
• Fix exporting multiple planes from single image by @yoda-vid in #611
• Bump certifi from 2023.7.22 to 2023.11.17 in /envs by @dependabot in #602
• Bump imageio from 2.32.0 to 2.33.1 in /envs by @dependabot in #608
• Bump pillow from 10.0.1 to 10.2.0 in /envs by @dependabot in #610
• Round-up of 2D plot fixes by @yoda-vid in #612
• Fix running Mayavi on Windows by @yoda-vid in #618
• Bump rich from 13.6.0 to 13.7.0 in /envs by @dependabot in #614
• Bump scipy from 1.11.3 to 1.12.0 in /envs by @dependabot in #615
• Bump matplotlib from 3.8.1 to 3.8.2 in /envs by @dependabot in #616
• Restore image settings during refresh by @yoda-vid in #613
• Bump pywavelets from 1.4.1 to 1.5.0 in /envs by @dependabot in #619
• Bump idna from 3.4 to 3.6 in /envs by @dependabot in #620
• Bump pandas from 2.1.2 to 2.2.0 in /envs by @dependabot in #621
• Fix ROI Editor margin and plane number by @yoda-vid in #622
• Bump tzdata from 2023.3 to 2024.1 in /envs by @dependabot in #623
• Bump pygments from 2.16.1 to 2.17.2 in /envs by @dependabot in #624
• Bump importlib-metadata from 6.8.0 to 7.1.0 in /envs by @dependabot in #628
• Bump pillow from 10.2.0 to 10.3.0 in /envs by @dependabot in #629
• Workaround for Apple Silicon platforms by @yoda-vid in #634

Full Changelog: v.1.6b3...v1.6b4