Magellanmapper

Changes

Installation
- Installs SimpleElastix binaries from a custom respository instead of SimpleITK
- Provides option to install optional dependency groups during in setup.py
- Venv setup script defaults to installing all optional dependencies
- Conda setup script uses `clr` as the default name again since the name can be customized
- Matplotlib ScaleBar is no longer required

Atlas refinement
- Updated profile modifiers for new pipeline nomenclature
- Adds metric for DSC of the labeled hemisphere
- Saves volume level stats to the imported atlas directory for easier access
- Stats output removes NaN columns for smaller files
- Labels interior-border images are now optional

Atlas registration
- Option to specify similarity metric

I/O
- Fixed missing interval when exporting a stack of separate image files

Server pipelines
- Finds NVMe devices assigned to a given device name

Python stats and plots
- Fixed colorbar labeling from command-line
- Fixed line plots with more line groups than styles and prioritize a solid line for the final group

Dependency Updates

Python Dependency Changes

- SimpleElastix installed from custom PyPi repository on GemFury instead of SimpleITK from official PyPi
- awscli and boto3 installed by default in Conda environment spec
- Default Conda environment name is changed back to `clr` when using the setup script
- Added PyQt5 and SimpleITK as required dependencies in setup.py, with SimpleITK version specifieid to get custom SimpleElastix in place of the standard SimpleITK, assuming extra-url flag is added to pip install to find respository
- Optional dependencies in setup.py for AWS, import, and miscellaneous graphics
- Matplotlib ScaleBar now optional
- Venv setup scripti installs dependencies based on setup.py rather than requirements.txt
- Updated `requirements.txt` to current snapshot and added an equivalent `environment_full.yml` Conda spec

Server dependency Changes

- nvme-cli required to map EBS volumes in NVMe-based instances to the correct drive path

Changes

Installation
- Ease Windows compatibility: SimpleElastix can be built with a batch script, docs on setup requirements, Bash setup scripts optional
- Allow a complete Conda environment installation from a .yml file
- Script for Venv setup with dependencies installation by requirements.txt file
- Specified required dependencies in setup.py
- Python-Bioformats/Javabridge and thus Java are now optional
- Shift most dependencies to Conda to make compiler optional

GUI
- Option to keep colormaps consistent with the original labels image
- Fixed intensity normalization for newer versions of Mayavi (>= 4.7)
Atlas refinement:
- Fixed lateral edge extension to extend only from labeled areas to avoid extending artifacts
- Decreased ADMBA E13.5 and E15.5 atlas thresholds now that artifacts are not being followed
- Minimize closing filter used to close ventricles in several ADMBA atlases

I/O
- Fixed error when displaying metadata after image import to Numpy format with newer Numpy versions (eg >=1.16)

Pipelines
- Option to avoid showing log output in nohup wrapper script
- Fixed potential to initiate a server command for the next rather than the current run script

Nuclei detection
- Removed deprecated anisotropic kernel settings

Python stats
- Make scatter plots cleaner by not splitting on different labels and giving an option to show only a single value from arrays in scatter plots to simply ROC curve labels
- Allow additional region metric groups, including those performed across whole super-structures rather than through weighted averaging
- Plot regional volumes and compactness across development
- Fixed line plots with more than 10 lines
- Extended scientific notation to line plots, format units with math text, use y-axis command-line-specified labels in bar plots, and allow turning off command-line labels for specific axes
- Quantify unlabeled hemispheres by volume and fraction of sagittal planes"

Dependency Updates

Python Dependency Changes

- Conda installs from Conda-Forge over defaults, with strict channel preference if using the setup script
- `setup.py` specifies required dependencies
- `setuptools` essentially required for `setup.py` (attempts to fallback to disutils but will fail when trying to find packages)

Changes

I/O
- Support `--prefix` when loading registered image files

Nuclei detection
- Replace verification method with Hungarian algorithm, which gives: 1) better optimized pairing of detection and ground truth, 2) fixes dependence on blob order, 3) is based on Euclidean distance rather than merely a bounding box
- Fix grid search/ROC formatting for arrays

ROI editor
- Refactor into separate module and classes
- Restore white color for all draggable circles to improve their visibility
- `bone` profile for bluish-greyscale high-contrast colormaps
- Fix display of blob verification matches above and below the ROI

Atlas editor
- edit button to toggle editing mode without a keyboard (`w` shortcut to toggle; `alt+click` no longer required/supported for editing)
- text box to input new label colors and provide feedback on selected colors

Image transformations
- `--transform` command-line parameter to specify image rotation and flipping
- Fix applying `--flip` argument to image export

Changes

Atlasing
- Enabled save button only with unsaved edits
- Tool to convert ITK-SNAP labels description format to CSV importable by Clrbrain
- Option to treat specific labels' corresponding histology regions as foreground for DSC to account for ventricular labels in E11.5
- Option to turn off lateral extension/mirroring completely while still using them to crop the output atlas

Image registration
- Save basic stats such as DSC after image registration

Nuclei detection
- Added `4xnuc` profile with size parameters for 4x microscopy

Python stats
- Bar plots: option to weight bars, more robust layout tightening and label placement
- Scatter plots: fixed grouping by multiple columns
- Saved peak smoothing qualities to CSV
- Added total intensity metric

R stats
- Jitter plots: allow different number of subgroups per group, fixed displaying multiple sets of paired data in the same plot
- Grouped metadata columns in output and simplified adding new metadata
- Fixed p-value extraction for correlation coefficient matrices"

Changes

Visualization
- Automatically generate colormaps for all channels
- Equalize transparency for all channels
- Invert 3D visualization along the x-axis for same "handedness" as in Matplotlib images

Image import
- Fixed regression in importing TIFF images to Numpy/Clrbrain format

Atlasing
- Option to merge images into separate channels
- No longer display images with registration suffixes unless explicitly specified
- Fixed regressions in atlas rotation during import

General stats
- Measure coefficient of variation
- Option to reverse order of conditions

Python stats
- Use nuclei for weighted averaging of nuclei-based measurements
- Library function for generating probability plots
- Configurable bar plots labels, vertical spans to further group bars

R stats
- Fixed regressions in jitter plots with mean summaries, single genotypes, unitless labels

Clean-up
- Removed obsolete volume and density functions
- No longer merge distance images

Changes

Server management
- Support swap file setup and loading
- Remove default NVMe device paths since they are not stable

Blob detections
- Reduce default blob chunk size to 1000 to reduce memory requirement

Atlasing
- Decrease erosion fraction to 50:50 for interior-border match metrics

R stats
- Correlation coefficient calculation and matrix visualization
- Normality testing"

Dependency Updates

R Dependency Changes

- Hmisc
- corrplot