Quality of Life Features and Bug Fixes

New Features:

• Fullscreen can be requested from menu
• Populations that aren't visible aren't shown on the plot
• Improved segment highlighting on the image
• Added segment search functionality to the image controls pane
• Population table hight increases if plot pane is closed
• Image renderer increases in size if population table and plot pane are closed
• Background is now black if all markers are turned off
• Segment features in legend are transformed if plot statistics are transformed
• Renderer image export includes a CSV with information about channel to marker mappings and threshold values
• Users can import and export region tiffs with CSV containing region names.
  • Expects A CSV in the same directory with the same filename (with a .csv extension instead of .tiff) as the labeled region tiff.
  • The CSV should have the format region_id, region_name

Bug Fixes:

• Fixed choppy fullscreen zoom
• Population graphics were all being regenerated on any population updated

Optimizations and bug fixes

New Features:

• New modal to choose which segment features are calculated
• New types of segment features added
• Added automatic update functionality

Improvements:

• Image renderer optimizations to improve speed and reduce WebGL context loss crashes.
• Segment outline optimizations to improve speed and reduce WebGL context loss crashes.
• Update Electron to v17
• Update Webpack to v5
• Dependency updates

Bug fixes:

• Fixes a bug where segmentation files stored outside of the image folder for individual images wouldn't load.
• Fixes a bug where where Mantis wouldn't restart on a crash.
• Fixes a bug where zoom wouldn't work when the mouse was being moved.
• Fixes a bug where region tiffs wouldn't load unless segmentation had been loaded.

v1.20-beta.5 - Project Population CSV Colors

• Project population CSVs can now be imported with an additional column for hex color values (must be in the format 0xffffff).

v1.2.0-beta.4 - Optimizations and bug fixes

• Replaces old segmentation line drawing method with more efficient method.
• Updated behavior for changing the lower end of the brightness slider to match other imaging analysis software.
• Updated imaging library geotiff.js
• Added the ability to import rudimentary gates from CSV. Not documented yet as we are planning to change the format.
• Bug fixes

User Experience Improvements

Overview

This release is primarily focused on improving Mantis Viewer's user experience. There are some new features in this release, but most of the work for this release went into improving the stability and usability of Mantis Viewer. Full release notes follow.

New Features

• Segment stats (i.e. segment id/number, and currently plotted segment features) displayed on legend for moused over segment.
• Added log scale for scatter and density plots.
• Mantis Viewer now calculates segment area in addition to mean and median marker intensities.
• Users can create population from a range of segment feature values.
• Population names and colors can be displayed in the legend.
• Added support for Ionpath MIBI TIFF file format.
• Users can import segment features for project from multiple CSVs stored in image directories (one per image directory).

Interface and Experience Improvements

• Mantis Viewer will now recover from most errors by restarting the application and reloading the previous project and image.
• Mantis Viewer displays a message in place of an empty renderer if no markers are selected.
• Image sets renamed to images.
• Plot feature selection dropdown displays message if no features are present in the database.
• Plot is replaced with a button to generate segment features if no features are present in the database.
• Image dropdown is now in natural sort order.
• Users can configure if segmentation is automatically loaded when switching between images.
• Users are now prompted if segment features that are being imported or generated will conflict with existing segment features.
• Clearing segmentation data will now also clear segment features from the database.
• Users are no longer asked if Mantis should recalculate segment features.
• Users will only be prompted to calculate segment features when exporting for project if some images are missing features in the database.
• Added support for importing from CSV files with .txt extension.
• PNG exports of renderer are named after the active image by default.
• Users can now control the number of bins for the histogram.
• Users can configure if Mantis scales or directly copies the channel brightness levels when switching between images.
• Project populations imported from CSV are imported with the same color.
• Users can choose to calculate segment features on a per image basis or for the whole project as part of the project import wizard.
• Users can cancel long running segment feature tasks (i.e. generation, import, and export for a project).

Optimizations, Bug Fixes, and Developer Improvements

• Renamed master branch to main.
• Separated webpack configuration for development and production builds and added production optimizations.
• npm start now makes use of electron-reload-webpack-plugin to rebuild and restart the application whenever a file is changed.
• Significant refactor of segment feature generation and import pipeline.
• PixiJS image and segmentation rendering optimizations.
• Marker and segmentation textures removed from GPU when switching images.
• All database requests moved to Web Workers to improve UI responsiveness.
• Optimizations with importing segmentation data.
• Added indexes to SQLite database to improve segment feature fetching speed for very large projects.
• Lots of little bug fixes.

v1.1.0-beta.2 - Bug fixes!

• Allows opening .txts in place of .csvs
• Fixes bug where toggling selection visibility did not work.
• Disables selecting populations on plot when downsampling is enabled as it was broken. Will be fixed and returned in a later release.

v1.1.0-beta.1 - Lots of new features and bug fixes!

• Now feature complete for v1.1.0
• Bug fixes and workflow improvements for importing new projects
• Regions of interest can be imported from a labeled tiff using the same format as a segmentation tiff.
• Regions of interest can be exported to a labeled tiff.
• Regions of interest and populations are saved to a database and are persisted between sessions.
• Image display settings are saved to a database instead of being saved to a separate file.
• Segment features (e.g. mean and median segment intensity) are saved to a database and are persisted between sessions.
• Users can load custom segment features from CSV
• Users can plot segment features across entire project instead of being restricted to just the active image set
• Users can toggle and configure downsampling of data for plotting.
• Users can toggle non-active image sets being collapsed when plotting for a whole project.

Project Import Wizard and Image Set Subdirectories

• Adds an import wizard to simplify the process of importing a new project with all of the associated metadata
• Adds the ability to have image files stored in a subdirectory of the image set

More bug fixes

Fixes a couple of minor bugs with importing populations, importing segment features, and loading segment feature data.

Minor bug fixes

• Possibly fix image blurring
• Small bug fixes to importing segment/cell features from CSV