MagellanMapper v1.5 Release Notes

MagellanMapper v1.5.0

Highlights

This release brings many enhancements aimed at creating a smoother user experience. Key changes include:

  • We overhauled the profile panel to preview each profile and show the currently loaded settings

  • Window sizes and positions are now saved between sessions

  • Image brightness-related settings are saved while scrolling through image planes

  • On Windows platforms, we now support all major atlas refinement tasks

  • Atlas smoothing supports adaptive kernel sizes per region and improves stat output

  • Newly generated atlases now collect labels metadata to make the atlases more portable

  • Image import supports single-plane RAW images and provides more feedback

Changes

Installation

GUI

  • Profile panel overhaul (#66)

    • Preview profiles before adding them

    • Skip the “Load” step; profiles are automaticaly loaded when added

    • View the complete settings for all loaded profiles

    • Clearer and more compact labels and button arrangement

    • Settings panel for resetting preferences and finding version information

  • Window size and position are saved as user preferences

  • The default window size is smaller to fit into 720p displays

  • The default focus is no longer the main image file path to avoid accidental file loading

  • Registered image selectors are now more compact

  • Fixed image intensity values and auto-adjustment to persist for each channel while scrolling and switching among channels (#76)

  • Fixed to retain opacity settings for borders images while scrolling (#79)

CLI

See the table of CLI changes for a summary of all changes in v1.5

  • Multiple processing tasks can be given in the same command; eg --proc detect coloc_match (#30)

  • Image preprocessing tasks have been integrated into --proc, no longer requiring a separate ROI profile; eg --proc preprocess=rotate

  • The new --prefix_out flag allows customizing output paths when --prefix is used to modify input paths (#73)

Atlas refinement

  • Adaptive kernel sizes can be used for smoothing operations (#53)

  • Metadata for labels images are saved when importing an atlas and registering the atlas to another image so that the original atlas no longer needs to be available (and --labels argument does not to be given) when loading the atlas or registered image (#65, #67)

  • Smoothing metrics are output during the --register merge_atlas_segs task (#51, #54)

  • The atlas profile settings meas_edge_dists and meas_smoothing turn off these metrics to save time during atlas generation, and the profile fewerstats turns off both these settings (#31)

  • Multiprocessing is turned off for lateral extension for better performance

  • Labels difference images, which map metrics for labels onto the labels themselves for data visualization, can now take specific metric files and columns from the included R package (#73)

  • Labels referencs loaded from CSV files now support level, abbreviation, and parent ID columns (#61)

  • Fixed multiprocessing tasks with SimpleElastix 2.0

  • Fixed DSC metrics between the atlas and its new labels, and more DSC metrics are saved (#57)

  • Fixed exporting labels reference files when a label ID is missing (#61)

Atlas registration

  • Image masks can be set to focus the field for image registration. Use the new --reg_suffixes fixed_mask=<suffix-or-abs-path> moving_mask=<suffix-path> command-line sub-arguments to load these mask files. (#40)

  • Register multiple atlases at a time, applying the same transformation to each of them. Specify additional atlase after the first, with output paths specified as prefixes, eg: ./run.py <sample-path> <atlas1> <atlas2> --prefix <atlas1-output-path> <atlas2-output-path>. (#69)

  • When registration fails, it will attempt to match more image parameters such as spacing and direction as fallbacks (#71)

Cell detection

  • Previously saved blobs are no longer loaded prior to re-detection

  • More flexibility when loading databases with blob truth sets

  • Grid searches support output path modifiers

  • Fixed blob segmentation and showing labels when none of either are present

  • Fixed exporting ROIs

Volumetric image processing

I/O

  • Improvements to loading registered images

    • The main image is no longer loaded if a registered atlas image is given

    • Images can be specified as absolute paths using --reg_suffixes to load any image, including those registered to another image (#36)

    • Images loaded for edge detection can be configured using --reg_suffixes

    • Files with two extensions (eg .nii.gz) are supported

    • Files modified by --prefix can now also be found in the registered image dropdowns

    • More support for CSV format reference files

  • Improvements to image import

    • Single plane RAW images can be loaded when importing files from a directory, in addition to multiplane RAW files (#32)

    • Skips single plane files that give errors (eg non-image files in the input directory) (#83)

    • Provides import error feedback in the GUI (#83)

    • The known parts of the import image shape are populated even if the full shape is not known

    • The Bio-Formats library has been updated to support more file formats (from Bio-Formats 5.1.8 to 6.6.0 via Python-Bioformats 1.1.0 to 4.0.5, respectively) (#70)

    • Fixed to disable the import directory button when metadata is insufficient

    • Fixed to create parent directories when importing images (#44)

    • Fixed to create default resolutions even when none are specified (#44)

  • Improvements to exporting image stacks

    • Images can be exported to multiple separate figures (#68)

    • Sub-plots are labeled

    • Image rotation arguments are applied (#50)

    • Plane index is only added when exporting multiple planes

  • Fixed to update metadata files when loaded through the --meta flag (#35)

  • Fixed error when unable to load a profile .yml file

Server pipelines

  • Continuous integration has been implemented through GitHub Actions to improve quality control (#55)

Python stats and plots

  • Scatter plot updates

    • Annotation columns can be names of index columns

    • Colors can be specified

R stats and plots

Code base and docs

  • Multiprocessing tasks are now more widely supported in Windows (spawn start mode), including the --register import_atlas, make_edge_images, merge_atlas_segs, vol_stats, and make_density_images tasks (#60, #68)

  • Type hints are now being integrated, replacing docstring types for better typing info and debugging (#46)

Dependency Updates

Python Dependency Changes

  • Python-Bioformats has been upgraded to 4.0.5 and uses a custom package that uses the existing Javabridge rather than Python-Javabridge to avoid a higher NumPy version requirement

  • Workaround for failure to install Mayavi because of a newer VTK, now pinned to 9.0.1

  • Matplotlib >= 3.2 is now required

R Dependency Changes

Server dependency Changes