MagellanMapper v1.3.0

MagellanMapper v1.3.0

This release brings many changes including a unified graphical interface. We also cleaned up the command-line interface (CLI) to make it slightly simpler and more flexible. Please note that several options have changed, which may require updating custom scripts. The sample commands script (bin/sample_cmds.sh) has been updated to illustrate this usage.

Summary of CLI usage changes:

Old	New	Purpose
python -m magmap.xx.yy	run_cli.py	All command-line based entry points can be accessed through the CLI using this script
Use atlas profile for registration	No longer needed	Atlases should be fully imported before image registration, and the atlas's profile should no longer be typically given when registering an image
--stats	--df	Run data-frame (eg CSV file) tasks
--roc	--grid_search <name1>[,name2]	Its main task is to perform Grid Search based hyperparameter tuning; specify profile names or YAML files
--rescale	--transform rescale=x	Grouped with other transformation tasks
--microscope <name1>[_name2]	--roi_profile <name1>[,name2]	Specifies profiles to process by regions of interest; delimit by , to allow underscores especially in file paths
--reg_profile <name1>[_name2]	--atlas_profile <name1>[,name2]	Specifies profiles for atlases; delimit by , to allow underscores especially in file paths
--saveroi	--save_subimg	Consistency with "sub-images" as parts of images that can contain ROIs
--chunk_size	None	Obsolete
finer atlas profile	None	Its settings are now default
--res	--set_meta resolutions=x,y,z	Grouped custom metadata settings into --set_meta
--mag	--set_meta magnification=x.y	Grouped custom metadata settings into --set_meta
--zoom	--set_meta zoom=x,y,z	Grouped custom metadata settings into --set_meta
--no_show	--show 0	Show with 1
--no_scale_bar	--plot_labels scale_bar=1	Grouped with other plot labels controls
--padding_2d	--plot_labels margin=x,y,z	Grouped with other plot labels controls, adding margin as space outside the ROI
--border	--plot_labels padding=x,y,z	Duplicated by the padding argument

Changes

Installation

• New Windows install script
• The install scripts are now the recommended installation pathway
• Install scripts perform silent Miniconda installs after prompting
• Fixed the URL for Miniconda download
• Fixed the run script to include command-line arguments

GUI

• All new integrated graphical interface with unified ROI Editor, Atlas Editor, and 3D viewer in separate tabs alongside the controls panel
• ROI Editor
  • Overview plot zooming scales to the size of the ROI
  • Orange border highlights the ROI z-plane corresponding to the overview plots
  • Shows similar pixel information as in the Atlas Editor
  • Layout now respects labels
  • Title now specifies axes
  • Title and empty ROI plots compatible with dark theme
  • Halve the size of truth blobs in verification plots to avoid obscuring the underlying image
  • Easier to flag detections in the ROI Editor
• GUI image loading
  • Load sub-images through the GUI
  • Fixed loading the GUI without an image
  • Fixed loading images through the GUI
  • Fixed image coordinate limits after loading an image
• Region selection
  • Option to select multiple regions, separating IDs by ,
  • Selecting a region ID shows its basic measurements
  • Fixed potential for label boundaries to exceed image boundaries
• Isotropic rescaling is turned on by default for 3D visualizations and incorporates image resolution
• NaN values can be used for invisible pixels, which reduces opacification when highlighting an atlas label in the ROI Editor
• 3D surface rendering is now default
• Unified save button for all viewers
• Auto-select a channel when restoring an ROI based on saved blobs' channel
• Fixed hang when opening the Atlas Editor for large images (downsamples images if necessary)
• Fixed error when showing an image with the z-offset set to the maximum value
• Fixed clearing picked colors during atlas painting
• Fixed the aspect ratio for images rotated 90 degrees
• Fixed display of RGB values for labels
• Fixed over darking some text boxes when hovering
• Fixed blob alignment in 3D surface rendering

CLI

• The CLI now serves as a unified entry point to the Command Line Interface, incuding register, plot_2d, and other tasks,
• The CLI can be accessed through the run_cli.py script, which benefits from the environment setup in run.py without loading a window
• --proc preprocess option to preprocess whole images by tasks specified in a preprocess ROI profile setting
• Many more sample commands for common tasks
• Better support for using the sample commands script without modification
• Help information added for command-line arguments
• Command-line arguments are checked for valid options when available
• Task to export image planes to separate files (--proc export_planes)
• Fixed sample commands for sub-images
• Fixed sample commands path setup for older versions of Bash (< 4.3)

Atlas refinement

• Resize images using the --size argument as an alternative to a profile setting
• Atlas operations expecting symmetry have been generalized across any axis
• Apply adaptive histogram equalization (access as a preprocessing task)
• Records total volumes of atlas and labels during atlas import
• Fixed rotation with resizing for non-z axes
• Fixed storing image plane boundaries for label contour interpolation

Atlas registration

• The atlas is assumed to be pre-imported, which avoids redundant atlas import tasks
• Support for more pre-registration atlas pre-processing tasks, such as 3D rotation, inversion, cropping, and rescaling
• Saves a truncated labels and pre-curated images only if the corresponding options are set
• Option to rescale units (eg mm to microns)
• Settings are customizable for each registration transformation task (eg translation, affine) rather than globally
• Defaults to increased b-spline iterations
• Fixed display of images through SimpleITK after registration

Volumetric image processing

• Grid Search profiles
  • Configurable as YAML files
  • Fixed Grid Searches without sub-image parameters
• Provides basic detection accuracy stats when saving blobs
• Option for whole-image contrast limited adaptive histogram equalization (using scikit-image)
• Fixed retrieving saved ROIs from the database

I/O

• Import from a directory of images
  • Option to convert RGB images to grayscale when importing images from a directory
  • Import multi-channel images
  • Fixed importing large images
• Option to specify output paths when importing a image directory or multi-page TIFF
• Can load multi-page TIFF files without channel indicator
• Defaults to saving figures as PNG
• Library functions for listing, downloading, and uploading files in AWS S3
• Library functions for de/compressing and testing files using ZSTD
• Allows loading the main image from a registered image path
• Avoids loading a sub-image when saving it to avoid a hang
• Sample YAML profiles for blob detection, registration
• profiles folder is checked automatically when loading YAML profiles

Python stats and plots

• Command-line options for configuring markers (--plot_labels marker) and annotation columns (--plot_labels annot_col)

R stats and plots

• Simple R script to load and run stats

Code base and docs

• Licensed under the BSD-3 open source license
• Moved AWS cloud management to a separate document

Dependency Updates

Python Dependency Changes

• Javabridge custom binary updated for import fix on MacOS
• Removed redundant PyQt5 installation during Conda installs
• Workaround for VTK 9 incompatibility with currently Mayavi dependency