MagellanMapper v1.6.0

Highlights in v1.6.0 release

• Atlas navigation
  • Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
  • Atlas regions can be searched (see "Atlases > Region")
  • Atlas Editor orthogonal 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
  • New atlases can be downloaded through BrainGlobe (see the new "Atlases" panel)
• Installation simplification
  • Simpler entry point to launch MagellanMapper: mm
  • Available as binary wheel to install without requiring the source code
  • Faster, lighter installation with fewer required dependency packages
  • Extends support to Python 3.12 and defaults to Python 3.9 (note: this is the last release to officially support Python 3.6-3.9)
  • Supports ITK-Elastix for image registration
  • Fixed installation on Apple Silicon (Mac M-chip) platforms (#634)
• Tutorial: Jupyter Notebook for running common tasks

Major changes since beta 4

Further fixes for these features/issues:

• Jupyter Notebook as a tutorial for running various tasks in the CLI (#659)
• Expand continuous integration testing to both pinned and fresh dependencies across Python 3.6-3.12 (#682)
• ITK-Elastix is now supported for image registration (#682)
• Fixed for NumPy v2 (#680)

See the full release notes draft here for more details.

All Changes

Show details

• 6241874 - Bump project version to v1.6b4
• 2ecc2da - Fix regex specification for converting ITK-SNAP labels to CSV
• 9b57e77 - Bump project version to 1.6b5
• 0bdf480 - Bump Venv setup script Python version compatibility to 3.12
• 5a41c4a - Bump readme year to 2024
• 700a5c9 - Fix initializing RangeEditor in Python 3.12
• f54d51b - Docs update on quick install and vignette
• 02166ce - Fix CI for macos-latest supported Python versions
• 434e109 - Test CI without Python 3.12
• 5e2ece4 - Test CI with multiple dependencies in include
• 8a32358 - Test CI with fixed include/exclude for Ubuntu and macOS
• f6c23d1 - Bump ITK-Elastix to v0.19.2 to support macOS Arm64
• c7f1ed1 - Release notes for extending support to Python 3.12 (#640)
• 759db62 - --- updated-dependencies: - dependency-name: requests dependency-type: direct:production update-type: version-update:semver-minor ...
• edc8c72 - Bump brainglobe-space from 1.0.0 to 1.0.2 in /envs
• 71c0035 - Bump tifffile from 2024.2.12 to 2024.5.22 in /envs
• 531e5c1 - Fix deprecated access to Matplotlib colormap
• 8d72c4d - Fix converting slice argument of 0 to None
• 12afc3f - Fix conflict in colormaps naming
• 6a09fa6 - Fallback to earlier Matplotlib colormap access
• eee83ed - Show registration parameters when running ITK-Elastix
• 183dd2a - Deconstruct reg suffixes from rescaled/transformed image names
• ddcf3e7 - Update BrainGlobe Atlas API to v2
• ee20927 - Use older BrainGlobe Atlas API for Python < 3.9
• e404733 - Add more settings to example blobs ROI profile
• c73ef6c - Fix stale absolute coordinate columns in blobs archive
• 6278845 - Upgrade blobs archive for missing absolute coordinates
• f32d632 - Accept blob column enums when accessing values from a column
• 4337af9 - Add blob region column and update docs
• 7f60581 - Set up region IDs for blobs when loading them during image setup
• ef32735 - Turn off "Raw" 3D option by defaut
• cceda7b - Turn off on-the-fly blob detection in surrounding areas if blobs are given
• c7da12e - Reduce extracting surrounding blobs
• 1d436d0 - Move region feedback to the atlas panel
• 743a305 - Show 3D blobs for selected regions
• 6b97d13 - Fix type hint reference to BlobMatch
• f210ed5 - Allow layering multiple sets of 3D blobs
• ca7421c - Re-enable "Raw" 3D mode by default if no labels image is present
• 655a9be - Release notes on BrainGlobe Atlas API v2 update (#650)
• 0621904 - Release notes on selecting 3D blobs by region (#651)
• 4c99f3c - Bump fonttools from 4.51.0 to 4.53.0 in /envs
• a0172d7 - Fix crosshairs for Matplotlib v3.9.0
• f09a061 - Release notes for fixing crosshairs in Matplotlib v3.9.0 (#657)
• b886132 - Print CLI args at regular level
• d4d9c57 - Simplify warnings during region export
• 3f9870b - Find ontology file path from labels metadata when making labels level image
• 3745dc8 - Support specifying labels image for mapped metric image
• 4739c13 - Get children IDs from a table of label IDs with immediate parents
• fd0fe38 - Release notes for simplified mapping metric to labels image (#658)
• 568ff8f - Fix np.lib reference for NumPy v2 release
• 39f9617 - Release notes for fix for NumPy v2 (#661)
• 6211658 - Bump urllib3 from 2.2.1 to 2.2.2 in /envs
• eeb0ae6 - Bump scikit-image from 0.22.0 to 0.24.0 in /envs
• 4bed64a - Bump certifi from 2024.2.2 to 2024.7.4 in /envs
• 23fe1ad - Bump zipp from 3.18.1 to 3.20.2 in /envs
• e738f8f - Bump fonttools from 4.53.0 to 4.54.1 in /envs
• bf140fb - Release notes for fixing region RGB export (#675)
• 3d48162 - Fix region export RGB values
• d186bdb - Fix colormaps' corresponding negative labels for NumPy v2 type casting
• fd94711 - Add sample commands Notebook navigation
• 34ea142 - Demo command for exporting map of regions to parents
• 624bdb8 - Add Notebook anchor tags for navigation
• 50a0bb9 - Add more image export example commands to Notebook
• 4a05b0e - Fix parsing "none" for --slice
• 6e9d6d3 - Release notes for adding navigation pane to Notebook
• 34b32f7 - Fix discrete colormap generation for
• 6b821fb - Release notes for fixing discrete colormaps for single-label images
• 21dbe5f - Pin ITK-Elastix to v0.20
• 8e479bd - Update requirements for 2024-12-22
• 0d1f195 - Pin PyQt5-Qt5 for all major platforms
• 2e8f499 - Fix CI for Ubuntu 24.04 libglx dependencies
• 9ce884d - Fix CI for Python 3.7 removal from Ubuntu 24.04
• 71b80e9 - Release notes for ITK-Elastix 0.21 workaround
• 21c5bd0 - Increase max Dependendabot PRs
• 51fec06 - Fix Dependabot open PR limit syntax
• 02367d1 - Version bump to v1.6.0
• b69d015 - Release notes for v1.6.0
• 468e32b - Bump year

Full Changelog: v.1.6b4...v1.6.0