Release Notes
1.5 - Aug 24, 2020 (v 1.5)
Improvements:
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
Maintenance and fixes:
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.
1.4 - May 18, 2020 (v 1.4.0.5)
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.
1.4 - April 20, 2020
What's New:
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
1.3 - January 27, 2020
What's New:
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
Maintenance and fixes:
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
1.2.0.292 - October 7, 2019
What's new
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
Bug fixes
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
1.1.1.285 - August 16, 2019
Bug Fixes
Error in saving analysis state after experiment reopening.
Application freezes after a series of actions performed on gating.
1.1.0.284 - August 12, 2019
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.
Bug Fixes
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
1.0.279 - June 17, 2019
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
1.0.270 - June 3, 2019
What’s New
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
Bug Fixes
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
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