Release Notes

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