MagellanMapper v1.1 Release Notes

MagellanMapper v1.1.4

Changes

GUI

  • Theming capabilities, including default and dark themes

  • Workaround for error if 3D points contain invalid values

  • Workaround to show labels when the first image displayed has no labels

  • Detection sphere slider is larger by making the max value compact

  • Fixed settings for overlaid multichannel images, allowing scalars in addition to sequences

  • Larger radius to select each ROI Editor draggable circle

  • Customize the number of serial 2D plot columns using the --plot_labels layout option

  • ROIs without any blobs can be saved

  • Truth blobs in verified plots are shown with their actual radius rather than as a fixed size and placed below detection blobs

CLI

  • Added “”.py”” extension to run script to allow cross-platofrm launch by double-click

  • Fixed detecting and activating Conda and Venv environments in the run script

  • Explicitly set truth database takes priority over the default path

Atlas registration

  • No longer specifies left/right for each label since the laterality may change with mirroring

  • Test profile without any registration iterations

  • Alternate output paths can be given as directories in addition to full paths

  • Fixed regression in generating a new atlas

Nuclei detection

  • Simplified setup for varying values at a single index during a grid search of a hyperparameter as an array

  • Total variation denoising weight is configurable

I/O

  • Default zoom and magnification values are now 1 rather than -1, and total magnification is always shown as a non-negative value

Server pipelines

  • Option to specify the plane orientation

Python stats and plots

  • Shift ROC legends to the lower right to reduce the chance of obscuring data points

MagellanMapper v1.1.3

Changes

GUI

  • Open multiple Atlas Editors at the same time, including synchronized annotation updates

  • Fixed inability to open an ROI Editor when a non-editable window is open

  • Fixed error when attempting to show 3D blob locations without any blobs

  • Fixed error when showing some ROI Editor overview images

Nuclei detection

  • Grid search hyperparameters groups have been reorganized into selectable profiles

  • Fixed running grid searches/ROC curves with Pandas 1.0

  • Unsharp filtering and erosion can be turned off during image preprocessing

  • The vmin saturation settings is now configurable, similar to the vmax setting

  • The lower threshold factor for max scaling is now configurable to reduce false detections in low signal areas

  • Microscope profiles for minimal preprocessing and low resolution images

MagellanMapper v1.1.2

Changes

Installation

  • No longer requires Git, C compiler, or preinstalled Java

  • Startup script attempts to activate an environment if necessary, allowing the script to work from a double-click

  • Moved installation docs to a separate file and added table of specialized dependency requirements

  • Fixed Venv environment setup script

  • Fixed SimpleElastix Windows build script to use the Conda environment Python executable if available

GUI

  • Performance enhancement when viewing labeled images, especially for images with many colors

  • Shows path of image loaded during startup

  • Allows loading the ROI Selector without any image

  • Fixed VTK error window display on Windows

CLI

  • Removed unnecessary pipelines script options

  • Fixed shutdown error on Windows and explicitly shut down the JVM if necessary Atlas refinement:

  • Label fill function now interpolates more smoothly and no longer adjusts the originally edited planes

Nuclei detection

  • Fixed error when no blobs are found during verification against truth sets

I/O

  • Applies metadata after importing image to make it immediately available for use

  • Fixed regression in loading registered images

Dependency Updates

Python Dependency Changes

  • OpenJDK 8 is installed through the Conda pathway

  • Uses prebuilt Javabridge

Server dependency Changes

  • Git is no longer required since not accessing Javabridge from Git

  • C compiler is no longer necessary as long as prebuilt Javabridge works

  • Java is no longer needs to be preinstalled if following Conda pathway

MagellanMapper v1.1.1

Changes

GUI

  • show the file path in the Atlas Editor window

  • fixed loss of label visibility after setting the opacity to 0 and changing planes

Atlas refinement

  • profile for Allen CCFv3

  • use the resolution of the fixed image during registration if the initial registration fails to start

I/O

  • use FFMpeg for export to MP4 files for smaller files that can be opened by QuickTime

  • fixed TIFF import to match only files with TIFF extensions (eg .tif or .tiff)

  • fixed loading images by SimpleITK to select a single channel

Python stats and plots

  • option for image padding size

MagellanMapper v1.1.0

Changes

Installation

  • Changed name from “Clrbrain” to “MagellanMapper”

  • Default virtual environment name is mag

  • Support new style Conda initialization during Conda environment setup

  • Update reference Conda environment and Pip package specs

Atlas refinement

  • Default to use symmetric colormaps rather than separate colors for labels on opposite hemispheres

  • Export RGB values with colored cells in Excel file of region IDs for a given atlas Atlas registration:

  • Fix b-spline grid voxels setting in NCC profile

Python stats and plots

  • Merge Excel files into separate sheets of single Excel file

Code base

  • Reorganized all source modules into subpackages

  • Moved all shell scripts in root folder into bin folder