MagellanMapper v1.2 Release Notes

MagellanMapper v1.2.2

Changes

GUI

  • Fixed ignoring the Atlas Editor opacity slider setting when scrolling through planes

CLI

  • Sample commands script uses a separate file for paths to allow updating the command script without overwriting users’ custom paths

  • Files are found from custom data directories more reliably

Atlas registration

  • Fixed preserving negative labels

MagellanMapper v1.2.1

Changes

GUI

  • Atlas Editor uses command-line specified alpha values

CLI

  • Option to load microscope and atlas profiles through YAML files

  • Script with sample commands for various common tasks

Atlas refinement

  • Option to turn off negative labeling used to distinguish hemispheres

  • The origin will update after atlas cropping

  • Cleaned up profile settings for label edge extension and mirroring

I/O

  • Fixed image stack export to use the new sub-image settings

  • Applied workaround for exporting image labels where the first labeled plane is empty

Dependency Updates

Python Dependency Changes

  • PyYaml (already included with other dependencies)

MagellanMapper v1.2.0

Changes

Installation

  • These release notes are now included in the repository

GUI

  • Setting transparency in overlaid images is more configurable

CLI

  • Multiprocessing supported cross-platform by adding spawn support for Windows, which is also available and the new default in Mac; currently implemented for blob detection and image downsampling

  • Fixed shebang for most Python files

I/O

  • File naming simplifications: removed series string (eg 00000), fixed some extensions (eg NPY instead of NPZ for single value archives), clearer suffixes (eg blobs instead of info_proc)

  • Distinguished sub-images (specify by --subimg_offset and --subimg_size) vs ROIs (--offset and --size), which fixes many issues with saving/loading image and blob subsets

Server pipelines

  • Tile stitching script uses JAVA_HOME for Java by default

  • Fixed attempting to upload to S3 when directory is not set