Release Notes
- Float Populations frame between Main and Gating tabs
- Ability to set Random generator seed for X-shift clustering
- Optional Ribbon scaling in Circos plot
- Ribbon color scaling by logsOdd ratio in Circos plot
- Checkbox for "Reset markers" in Marker Manager
- Improved performance in Gating selected populations
- Improved exporting of the region image to retain digital zoom
- Addressed issues with 'Archive population' operation
- Resolved issues concerning Gating operations and handling of Saving/Opening Analyses
MAV 1.5 will be the last version to be supported on MAC OS.
Improvements and Bug Fixes:
- Improved handling of the features like Circos plot, Progress bar, Gating displays when using MAV 1.4 on MAC OS
- Fixed the clustering errors - errors associated with incorrect/unselected populations assigned to clusters.
Highlights:
- New!! Circos plot feature is replacing the spatial network graph for improved graphical representation of spatial interactions
- Improved User-interface
Improvements:
- Better organization within the main application window, e.g., sub-windows with default sizes organized in tab pages
- Region images display window moved into the main application window for better display organization.
- Column headers in the marker manager window are now anchored
- Changes to gated populations immediately displayed in the region images
- Scaling improvements to match zoom level with gating scatter points
- Added optional scaling of markers
- Populations now archivable
- Improved visibility of population interactions table
- Improved History window to display the source of the populations when the populations are created and renamed
- Added computation progress bar
Maintenance and fixes:
- Improved loading time for markers
- Dropdown menu options are now sorted alphabetically
- Addressed incorrect display of the plot of populations, where the overlap population persisted even after the removal of original populations
- Addressed incorrect display of regions when opening a saved analysis
- Addressed incorrect zooming using the “+” button
- Addressed the missing “Region row DND” button in population table
- Addressed the app freezing upon minimizing the markers window
- Batch Analysis - Ability to save analysis scheme and apply it to different experiments
- Spatial Heat maps to visualize cell type density
- Improved window management: separate tabs for clustering and analysis
- User-definable min/max distance for the Spacial Network Graph and Population Interactions features
- Status of the Population interactions operation displayed on the Background Activities panel
- Numerical sorting for marker column sorting
- The cell number of populations available in the CSV files
- Improved the right click pop-up menu with operations (creating population. removing an area, reverting area, exporting area)
- Simulated-DAB staining visualization mode available
- Analysis state doesn't open if analysis saved after closing all regions of experiment
- Cannot delete populations when working with a larger number of populations (over 100)
- Cannot create a child plot from a previous gate when working with the second region of the experiment
- For some populations, the gating analysis is not accurately saved
- Gating menu disappears after reopening analysis state with gating
- Error when zooming in and out of an image using “plus” and “minus” buttons
- Gating images remain in the memory of ImageJ after closing Codex MAV
- Signal intensities for a given cluster group change when moved to the population tab
- Resetting experiment doesn't work when choosing "No" during saving analysis state
- Gating:
- Display and create gates from histograms and column charts
- Ability to subdivide biaxial scatter chart into quadrant gates
- Zoom in plots using right-click and drag into the gating plot (axes range)
- Collapse and iconify gating windows
- Scrolling in gating windows is dependent upon screen resolution to ensure consistent UX
- Display all regions on gating window
- <-> button between X and Y to swap the axes
- Overlay manager:
- Scale bar overlay to show image dimensions
- Segmentation overlay is disabled by default
- Region image:
- Remove / exclude areas of a region image for subsequent analysis.
- Display specific marker intensity value in region image viewer for pixels
- Allow user to save a part of the region with ROI selection and visible markers and other overlays
- Experiment:
- Add prefix for names of saved analysis states
- Add a shortcut to Reset experiment to the file menu
- Select last modified processed and segmentation results by default
- Disable best focus feature for 2D experiment data sets w/ segmentation
- Add channel name = "Empty" to the check for disabling on marker manager by default
- UI:
- Display analysis history window by default
- Angular distance measure is selected by default for clustering
- Channel names column are pinned when scrolling down in clustering/population window
- Changes to context menu in Population table
- Ctrl K function on MAV does not open ImageJ intensity histogram window.
- Occasionally setting brightness and contrast automatically fails to work correctly in region window
- "Gating axis tick marks show non-integer values under normal circumstances
- TMA dataset failed to load on Windows Server with multiple ImageJ open
- Gating. Populations disappear from region image after the moving of gate on scatter chart
- MAV freezes / hangs while repositioning parent gate under certain circumstances
- Error in saving analysis state after experiment reopening.
- Application freezes after a series of actions performed on gating.
What’s New
- Main window:
- Main window title contains current analysis state name and application mode (online/offline)
- ”Open experiment” dialog is resizeable
- Region image:
- Option to display the best focus plane(s) of a region
- Size of region image window initializes to half of the screen
- Option to export Image from region window instead of ImageJ menu / toolbar
- Toggle tile number image overlay
- Populations:
- Export populations to CSV in addition to FCS
- Population combine functions (intersection, set difference, disjunctive union)
- “Add all” button in the cluster table to create populations from all clusters at once
- Ability to perform actions for multiple populations at the same time if selected together (color, visibility, deletion)
- Ability to gate populations
- “Selected” column name in Population List changed to “Visible”
- Gating:
- Keyboard shortcuts for gate deletion (“DEL”) and cancel in-progress gate (“ESC”)
- Ability to synchronize scaling across all scatter charts
- Option for arcsinh transformation
- Option to automatic rescale scatter chart when switching between regions
- Clustering:
- Ability to deselect all markers in marker table prior to clustering
- Cluster window title contains K-value
- Improve performance of FLANN version of X-shift by 2-5x
- Option to normalize clustered results using quartile binning
- Common:
- Capability to save table intensity data as CSV
- Heatmap tooltips display mean and standard deviation
- Option to export images in SVG format.
- Application freezes when the user tries to open an analysis state containing several selected markers
- “View” panel is hidden when viewing an experiment without segmentation results
- Error message during Voronoi diagram rendering after region switching
- “Close application” window is obscured by “Open experiment” window when closing application
- Cannot change servers within the same ImageJ instance
- Arrows in the gating show incorrect direction when parent gate is partially visible
- Experiments can't be closed if they don't have any populations
- Background activity message at times displays unrelated messages
- Gate exceeds the plot's boundaries after creation if it has intersecting sides.
- Intermittently, “Open experiment” menu item does not bring “Open experiment” window to the front
- Segmentation overlay is displayed temporarily when a region image is loaded
- Negative bounds of gates after the logarithmic scale application
- Server online mode : no error message shown if experiment is not available during mounting on MacOS
- Application freezes after canceling x-shift clustering run
- Incorrect auto-coloring and sorting of populations after the deletion of a population
- “Open experiment” window may not close after the closing main window
- Error message when saving experiment analysis state without segmentation
- Horizontal size of the table in clustering/population window is limited
- Scrolling clustering/population window is slow
- Cannot scroll in clustering/population window after clicking on a cell
- Marker Picker panel can be frozen after changing marker coloring multiple times
- Application hangs when creating multiple gates, child gates, and populations
- Gating: log / linear transformations do not always adhere to the min/max x/y settings
- Logs odd ratio calculation shows the same values for all clusters
- Populations are not visible on region image when a user open saved analysis state
- Oval gating changes size during scale change
- Changed coloring of populations resets after deleting some population
What’s New
- Option to normalize expression intensities during X-shift clustering
- Clustering options moved from preferences to clustering parameters window.
- Option to normalize X-shift clustering results.
- Population marker size limits changed to 3 - 30 and added new marker shape options
- Option to define a gate on a per region basis
Bug Fixes
- Performance issues in gating when selecting X or Y values from dropdown lists for very large datasets.
- Performance issues when starting gating on very large datasets.
- Gate polygons disappear when outside of boundaries of scatter chart.
- Incorrect behavior in gating when switching between logarithmic and linear scales
- Performance issues when loading a large experiment
- Delay when adding new populations if populations are displayed in a region image window
- Performance issues when toggling marker visibility
- Incorrect Voronoi vertices and polygon shape in regions containing large sections with no cells.
- Sorting of cycle column in marker manager is not based on a numeric sort order
- Unable to load clustering results for datasets containing more than one occurrence of the same marker name
- Auto-coloring of the populations according to their dendrogram ordering
- Auto-identification of K-value for X-Shift clustering
- Range validation for KNN value for X-Shift clustering
- Experiments and jobs in “Open Experiment Window” sorted by date created
- Dendrogram branches are spaced more equally
- Default population shape is now a filled circle
- Cannot open FlowJo and Vortex FCS output files
- Cannot start clustering under certain conditions
- Cannot open segmentation with an empty region
- Cannot sort by marker names in cluster marker select window
- Performance issues with zooming when populations are not visible
- Performance issues after adding populations
- Incorrect dendrogram display
- Incorrect scatter chart axis range validation for log-scale
- Incorrect use of visible vs. selected populations for clustering