# 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 {% hint style="warning" %} MAV 1.5 will be the last version to be supported on MAC OS. {% endhint %} ## 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