MagellanMapper v1.4 beta 2

We have fixed many issues related to the new installed packages, including errors on first-time launch. Our first Linux build is also included!

• Added Linux package, built on Ubuntu 16.04 and tested on 16.04 and 20.04
• Fixed crash when attempting to create a log file in a new directory
• Fixed crash when the JAVA_HOME environment variable is not set (this setting is not required for the installed packages)
• Fixed using the bundled Java runtime environment
• Fixed updating imported image metadata when both the metadata version number and file format need to be upgraded

These packages include all of the additional updates planned for our forthcoming v1.4 release. Please see the release notes for details on these changes. One major change is the addition of logging to file, especially necessary now that MagellanMapper from installed packages is typically launched without a console. Logs are output to out.log located in:

• Windows: C:\Users\<your-username>\AppData\Local\MagellanMapper
• macOS: /Users/<your-username>Library/Application Support/MagellanMapper
• Linux: /home/<your-username>/.local/share/MagellanMapper

Any and all feedback is welcome!

MagellanMapper v1.4 beta 1

Our first release with standalone installers! These packages contain a full environment without requiring use of the command-line. The Windows package includes a full installer including Start Menu integration. The macOS package contains an app bundle that can be dragged to Applications to run from the standard Launchpad.

As these packages are our first standalone releases, please do provide feedback on your install experience. More details on the changes in v1.4 in the release notes.

MagellanMapper v1.3.8

This is a bugfix release for MagellanMapper.

Changes

Installation

• Fixed missing dependencies required by Pyface Conda dependency

GUI

• Fixed incorrect color mapping for some corresponding labels (ie same region in opposite hemispheres)

Atlas refinement

• Fixed error in compactness measurement when no surface is found

Atlas registration

• Specify a full fallback atlas profile rather than only a fallback similarity metric if the post-registration DSC falls below threshold (metric_sim_fallback setting)

Cell detection

• Fixed applying the first channel's profile setting for image saturation to all channels during blob detection

I/O

• Fixed reading image size and resolution metadata when values for some dimensions are missing
• Fixed importing RGB images
• Fixed redundant channel import for some formats (eg some OME-TIFF files)

Dependency Updates

• Added import_metadata and import_resources packages required by Pyface

MagellanMapper v1.3.7

This is a bugfix release for MagellanMapper.

Changes

Installation

• Fixed launch error when Javabridge is installed but Java is not

GUI

• The "Save Figure" button opens a file save dialog to configure the location, filename, and file format of saved figures
• Fixed display resolution on HiDPI screens set to fractional scaling (eg 150%; the fix requires Qt 5.14+)
• Fixed Atlas Editor non-Numpy image initial loading performance (regression introduced in v1.0.0, most notably in larger images)
• Fixed Atlas Editor to enable saving after edge interpolation

CLI

• Configure DPI of saved images using --plot_labels dpi=<n>
• Specify colors for NaN values through --plot_labels nan_color=<color> instead of through --atlas_labels binary=<color>, which is now only specifies colors when displaying labels as binary images to fix this display
• Defaults to saving images in PNG format, even if --savefig <ext> is not set
• CLI sub-arguments are now shown in ./run.py -h (help documentation)
• Fixed saved plane filenames to use the plane index for the axis corresponding to the saved plane

Atlas refinement

• Smoothing metrics now include the filter size in metrics output
• Fixed the denominator in the smoothing displacement metric and smoothing metrics for non-existent labels

Python stats and plots

• Excludes decimal points that were likely included by floating-point errors
• Fixed mapping measurements to labels with weighting

MagellanMapper v1.3.6

This release focuses on usability fixes. New settings settings and build tools have been added to support older Linux platforms.

Changes

Installation

• Dockerfile based on Ubuntu 16.04 added to support running on older platforms

GUI

• Status bar shows pixel values in zoomed ROI plots
• Fixed upper/lower case in check box labels
• Fixed saving ROIs to use the original ROI offset
• Fixed resetting the labels opacity when scrolling through planes
• Fixed updating channels in the image adjustment panel for the current image type

CLI

• --cpus <n> command-line argument to specify the maximum number of CPUs to use for multiprocessing tasks
• ROI profile setting (mp_max_tasks) to set the maximum tasks per process, which can reduce memory usage considerably

Volumetric image processing

• Density heat maps default to using the whole image
• Fixed ROI saturation to use the max_thresh_factor ROI profile setting

I/O

• Better information when a file could not be found for import
• Specifying the profiles directory is no longer necessary when loading YAML profile files, including those in sub-directories
• Experiment names in the database now ignore any file extension

Dependency Updates

Python Dependency Changes

• SimpleElastix compilation
  • Dockerfile to build for older platforms
  • Allow directory to be given as a relative path in the build script
  • Fixed loading a library in the script
• Install Matplotlib >= 3.3.2 (in setup.py but not yet in Conda install script) now that the performance regression starting in 3.3.0 has been fixed
• Additional Pandas dependencies can be installed by specifying the pandas_plus group (installed by default in the setup scripts)

MagellanMapper v1.3.5

This release streamlines refreshing and overlaying images through the GUI. Workarounds are also provided for several installation/dependency issues.

Changes

GUI

• Multiple intensity images can be selected through the GUI to overlay
• Refreshes images in each viewer after a new image has been loaded
• Selecting an ROI dropdown menu entry updates the current viewer
• Fixed retaining prior images and resolutions from previously loaded image during the session
• Fixed setting the initially displayed channel from the command-line
• Fixed to show the labels reference file if loaded from command-line
• Fixed loading ROI Editor layouts with 3D screenshots if the 3D viewer had not been opened yet
• Fixed 3D viewer orientation when opening the tab for the first time during a session
• Fixed blob detections to appear in both the ROI Editor and 3D viewer

CLI

• Simplify loading only images by registration suffix to allow specifying a directory as such: --img <dir> --reg_suffixes [atlas-img] [annotation-img]

I/O

• Resolutions are easier to read with fewer decimal places shown
• Filenames are saved in the database experiments table without extension to allow more naming flexibility
• Fixed applying objective magnification and zoom metadata to multi-plane image imports

Server pipelines

• Removed default microscope objective metadata now that metadata is extracted from input files when possible

Python stats and plots

• Fixed loading discrete, symmetric colormaps with an even number of colors

Dependency Updates

Python Dependency Changes

• PyQt is now specified explicitly for Conda environment installs to avoid installing an older release (ie was installing v5.9 instead of v5.12)
• Matplotlib v3.2 is installed because of performance slowdown especially during mouseover of images when using the latest current release (v3.3)
• Fixed setup.py to include PyYAML (dependency introduced in MagellanMapper v1.2.1)

Server dependency Changes

• Dockerfiles are included, with one version based on Miniconda3 and another on Ubuntu 18.04

MagellanMapper v1.3.4

This release eases ROI setup and fixes a number of channel, import, and installer issues.

Changes

Installation

• The Conda setup script will initialize all shells for Conda, which fixes activation in zsh on macOS
• Initial Docker integration
• Fixed Conda light environment specification for the custom Javabridge pacakge

GUI

• ROI controls synchronize with the ROI and Atlas Editors
• ROI Editor
  • Preview a new ROI by clicking on a desired position in any overview plot
  • Redraw by double right-clicking in any overview plot
  • Changed the shortcut to jump to the plane of a given ROI plot: right-click the plot (instead of right-arrow + left-click)
  • Option to toggle detection circle visibility
  • Fixed ROI Editor title spacing
• Fixed channel indexing when selecting a subset of channels
• Fixed resetting labels images when loading a new image
• Fixed loading image filenames that partially match registered suffixes
• Fixed saving blobs when no blobs have been detected

CLI

• Fixed to apply alpha channel parameter when overlaying images

Atlas registration

• Fixed YAML atlas profile template for b-spline registration settings

I/O

• Selecting an imported file in the Import tab loads the file instead
• Fixed handling incomplete metadata during import

Code base and docs

• Provided uninstallation directions

MagellanMapper v1.3.3

This is a bug fix release for Conda setup.

Changes

Installation

• Fix Conda setup when conda is not found, including new installations
• Fix setting up a Conda environment when another matching environment is found from a different Conda installation

I/O

• Fix import of multi-file, single-channel RAW images

Python stats and plots

• Option to drop duplicates when joining data frames using the new --plot_labels drop_dups=<0|1> command-line argument

MagellanMapper v1.3.2

This beta release streamlines scripts to install and run MagellanMapper through a file browser, without requiring a terminal. Registered images can now be loaded and overlaid through the GUI. The image import panel auto-populates available metadata, and RAW format images can be imported. Image intensity controls better adapt to the current image.

Installation

• Conda setup script for Bash (eg Mac/Linux)
  • Creates a MagellanMapper launch script that auto-detects more python installations to launch run.py (ie when only python3 is available or if python is only available through Conda)
  • Better able to find existing Conda installations before attempting to install Conda
• run_cli.py has been re-integrated into run.py and removed

GUI

• Select registered images and labels in the ROI panel
  • Control the main intensity image, showing all available images registered to the current image
  • Selector for a registered labels/annotation image
  • Selector a labels reference file
• Import panel
  • Brings the user to the import panel when unable to load a file
  • Auto-populates metadata when available from the image file
  • Added output image shape and data type fields
  • Turn on all channel after when displaying a newly imported image
  • Fixed re-displaying an image re-imported to the same output path
• Image adjusment panel
  • Adapts the intensity range to the current image to allow finer adjustments
  • Option for auto-intensities
  • Fixed settings to persist when scrolling among planes
  • Fixed slider sizes by capping the size of number labels
  • Fixed intensity slider ranges for images that were not imported into Numpy format
• Blob detector controls have been moved to a separate "Detect" panel
• Fixed crash when selecting the 3D Viewer tab or detecting blobs without a loaded image
• Fixed updating ROI size when loading an image through the GUI
• Fixed decimal point display in integere

I/O

• Support for importing RAW image format files
• Export images to RAW format (--proc export_raw)
• Support for both TIFF and non-TIFF format files through Bioformats
• Fixed support for incomplete metadata
• Fixed importing images while skipping channels
• Fixed import when unable to load the main image

Server pipelines

• Fixed to not attempt download from S3 if an S3 directory was not set

MagellanMapper v1.3.1

This beta release contains multiple new control panels to adjust profiles, brightness/contrast, and image file import. These controls allow users to control MagellanMapper more graphically and reduces the need to restart for new settings.

Changes

Installation

• Keep Windows setup script open after installing by double-click to view instructions and any error messages
• MacOS/Linux Conda setup script renamed to allow double-click launch on MacOS and to further distinguish from the Windows setup script

GUI

• Control panels
  • Profiles panel: select, refresh, and reload profiles
  • Image adjustment panel: change brightness, contrast, and opacity
  • Image import panel: view and adjust matched files before import, add metadata, load immediately after import
• Select subset of channels instead of only all or single channels
• Zoom and pane functions in the ROI Editor overview image plots
• Adapts to high resolution (HiDPI) screens
• Consistent dark theme applied automatically when the system dark theme is used (depends on PyQt detection)
• Fixed crash when opening the Atlas Editor tab without an image loaded
• Fixed performance regression in ROI Editor

CLI

• --channel command-line parameter accepts multiple arguments
• Sample commands script prioritizes finding Numpy image files
• More error output from run scripts
• Fixed attempting to run MagellanMapper in the Conda base environment