CODEX® Support
Comment on page

Release Notes

1.5 - Aug 24, 2020 (v 1.5)


  • 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

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:

  • New!! Circos plot feature is replacing the spatial network graph for improved graphical representation of spatial interactions
  • Improved User-interface
  • 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 - 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 - August 16, 2019

Bug Fixes

  • Error in saving analysis state after experiment reopening.
  • Application freezes after a series of actions performed on gating. - 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