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