v4.x 2019

moves the Qf tree (Phenogram) and QF dissimilarity table+histogram to open source for MathWorks. They are now decoupled from the AutoGate Gui and invokeable from command line.

includes fixes and improvements based on Cytek presentation 
1) Cleans up problems with Phenograms in terms of text label positions, confusing frequencies when doing inter-sample MDS comparisons OR having overlapping subsets, syncing phenogram colors with highlighting colors and truncating title 
2) Cleans up QF and F measure histograms 
3) Avoids title truncation on 1D pathfinder from MDS display 
4) Add QF dissimilarity histogram and table to supervisors object

1)Handle bug where minimum distance for UMAP can be lost 
2)On supervisors legend window associated to the PlotEditor window for creating gates and DE-SELECT “New subset” and “unsupervised” when you initialize 
3)Avoid exceptions with small subsets

1)Fixes MAJOR exception navigating to a gate created by UMAP supervised templates which is matched by nearest neighbor alone 
2)Fix GatingTreeTable column alignment bug for FCS parameter statistics caused in September 2019 by addition of absolute cell count column

evolves multi-sample umap processing to be in sync with last 5 months of work on supervised templates and supporting python or MatLab. More stable now

1)Support supervisor highlighting in 3D umap output even if there are no dbscan clusters 
2)Attach supervisor window preference to current parameter reduction’s parent pid 
3)Turn OFF the epsilon GUI if no 3D selected

1) Reword Clusters checkbox “See DBM clusters” and if deselected hide cluster detail dropdown 
2)Ensure that 3D output is supported if user elects to use Python implementation by Leland McInness 
3)Optimize switching gate focus in PlotEditor when it is using Tsne or UMAP data. 
4)Minor bug fixes plus 80% complete with code for new type of manual gate: umap label gate. new manual gate type will open door for dbscan gate as well without disturbing DBM cornerstone which is needed for every 2D projection. 
5)Let “Create selected” button for supervisors be a default root pane button so ENTER is heard 
6)If a 2D plot is parameter reduced by UMAP with supervision THEN provide an orange wrench button at the top right of the ParameterReduction of PlotEditor window so that the user can quickly adjust legend preferences and change matching to supervising labels.Also put this same orange wrench button at the bottom right of the supervisor legend when it is a separate window 
7)Improve tool tips in PlotEditor and ParameterReduction windows 
8)If user selects a SINGLE checkbox for UMAP supervisor then FLASH the area in the plot that is associated to that supervisor. OTHERWISE do not flash if user deselects a checkbox or deselects/selects MULTIPLE checkboxes with ALL button 
9) MOST IMPORTANTLY …. stabilize the new type of AutoGate: Umap label gate. Make this a flexible basis for any type of gate in the GatingTree (xshift, dbscan, etc.)

Improves UMAP user interface by giving clearer advice on probability binning and by protecting the use of python templates for MatLab and vice versa

Umap python

Fix for Cytek samples and Stephen’s UMAP commits

Bug fix on TreeTable

1) Fix count display SO THAT if the number is LESS than 1000 it always shows as integer without the suffix ‘k” IF THE display preference displays 42531 as 42.5k or 45.53k 
2)Alter minimum logic for minimum cluster size per Wayne’s request 
3)Normalize scales before running QF match 
4)Ensure JAVA initializes if user runs example 10 of run_umap.m after starting up

Fixes last minute bug in window display

1) Makes usuer improvements for Nov 4 lab meeting slides 
2) Support high definition monitors when ispc on Microsoft Windows

Fixes “side effect” bug with creating phenogram that was caused by other changes in last 3 weeks.

1)adds new stochastic gradient descent options to UMAP 
2)adds QF match to UST (umap supervised templates) 
3)adds re-supervision examples to run_umap open source

1)Latest Epp logic for KLD from Wayne
2)Improve umap supervised templates to detect new subsets, warn and optionally re-supervise
3)Allow import of subsets from file format provided by Nikolay Samusik
4) Support a single version file for any matlab version or operating system that gets noticed by AutoGate WebUpdate.m for that release 

provides first draft of new UMAP feature “re-Supervised templates” which are done when a supervised template (training set) does not account for all likely populations in an applied-to sample (test set).

Refactor code to be more object oriented for 3D UMAP and dbscan cluster plots

provides GatingTree highlighting into 3D clusters

corrects some issues with 3D UMAP display

improves the handling of the fig3D window and supervisors window and fixes several bugs with the new UMAP 3D stuff., SIGH

improves UMAP 3D clustering

First draft of functionality to support 3D umap and dbscan. Not finished. Not certain that it will work. Sigh.

Preliminary support for r2019 a or b

adds new feature to shrink large FCS files acording to a marker expression minimum value on one or more parameters

contains new search ability on mnuMultiDlg

Improve functionality for sorting and searching

Allow user to open FlashLightDlg window on selected node of GatingTree window

1)Avoid exception when calling color highlighter dialog from MDS window when the unmatched subsets are HIDDEN
2)Allow user to say “No need” for creating lo res 1D PF and to remember this answer
3)Avoid constant message about orphans in MDS match table

1)Decouple open source from AutoGate by handling the need for global properties by open source towork through the BasicMap class’s static function Global. BasicMap.Global carries app dependencies in disguise by allowing its singleton to be externally set. Ensure compatibility in variables needed for MS windows high definition management. Ensure compatability in transmission of contentFolder location.
2)Support progress bar when creating 4 organizer classes from GatingTree. Organizer classes separate non automatic from automatic gates and any type of UMAP redcution for each other and from automatic and non automatic gates.
e)Add new search mechanism to Supervisors legend from UMAP and to every checkbox picklist served up by mnuMutliDlg

1)Improves handling of interactions between PlotEditor and java legend window for UMAP supervisor gates based on feedback from Connor Meehan
2)Improves MDS match table based on feedback from Connor Meehan
3)Allows user to quickly create organizer gates for informatics research

1)Handle edge case where all samples given to democratic W are below the minimum required events
2)When doing umap supervised support name differfentiation when subset names are identical. Justin noted that many gate names are identical inhis absolute cell count example sample (e.g. MCB log and MCB high). In such cases AutoGate uses parent gate name to differentiate when doing UMAP supervised parameter reduction for supervisor legend
3)Continued issues with dragging and dropping UMAP gates or Epp top gates to drop points with same events. Many combinations of dragging 1 or more gates to any drop point needed more testing. And affected PlotEditor windows MUST be closed. This operation is fundamental to organizing AutoGate’s gate types into separate sub-hierarchies at a peer level.

1)Code complete on absolute cell count feature
2)Allow UMAP gates to be dragged to a gate with the same events as the dragged gate’s parent. This helps in reogranizing the gating tree
3)Allow gate labels to be hidden/revealed in PlotEditor window.
This logic can be operated by a:
a)Button on java legend for UMAP Supervisors.
b)Right-click menu item that the genie search can see.
c)Tool tip when clicking on the label in the PlotEditor

1)Allow user to embed supervisors legend in plot window
2)Do not require UMAP python when user changes from tSNE to UMAP in dropdown\
3)Preliminary code for absolute count … not FINISHED yet

Fixes needed for the experiment of Nikolay Samusik

llows user to create gates for selections in Supervisors legend that shows when PlotEditor is viewing a UMAP reduction based on an AGUST (AutoGate UMAP supervised template)

1)Provides 2 fixes to problems found in UMAP’s original Python version
2)Close umap java legend window when PlotEditor navigates away from relevant focus
3)For the several checkbox “pick list” windows
i)ensure count is reflected in “All” checkbox as users select/deselect
ii)Support sorting and ordering on mnuMultiDlg and Supervisors java legend
4)Continue ensure CD sort where CD113 is greater than CD8 on heatmap and other pick lists

improves AGUST (AutoGate umap supervised template)
1) Ensure that each new subset possibility discovered by AGUST appears distinctly in the legend with slightly distinct gray-ish color and can be selected in plot and get tooltips in plot
2) With supervisor UMAP’s legend dialog using JCheckBox instead of JRadioButton make sure that the current ON/OFF state of gate showing is remembered every time the plot is refreshed!!
3)If user draws manual gate in supervised umap PlotEditor window find the closest/best supervisor name as a suggestion when creating the gate

1.New Epp tuning parameters:
a.Min KLD Test is same as before. Default is .25.
b.Min KLD stop condition. A 2nd minimum that discards all separatrices for a single 2D projection if it is below this minimum. Default is .08;
c.Min axis cut off ignores any cluster that is below a place on the measurement scale. For Cytof it defaults to 4.For FACS it defaults to -10 to catch over compensation.
d.Min axis drop down controls how/when to test cut off
2.When Epp resumes with different policy for trimming of leaf gates the old Epp leaf is removed to avoid confusion with overlapping gates when doing QF match
3.When transferring reagents between used and unused lists for Epp or look-ahead … mainning the marker CD sort where CD7 is less than CD161
4.GatingTree deletion no longer hides tree and deleting process with banner “Removing # gates”. This 5 year old approach took too long IF large Epp sub hierarchies are expanded.
5.When navigating PlotEditor to different pre-existing gate do not save any cluster selections as a new gate if the gate is Epp

GenieWiki updates/fixes and CSV2FCS conversion (disabled)

1)Fixes bugs created in last 2 days with sorting markers in list
2)Adds new histogram feature to MDS sort table for summarizing scores visually

improves time spent/remaining reports and fixes exception when using UMAP without a template

Supports gathering and using parameters from GatingTree selections from different samples in the Epp configuration window and the Parameter Reduction window (UMAP/tSNE). Both windows are non modal allowing user to pick in GatingTree.

Epp Config window’s “Use GatingTree parameters” link
1)has bug fixed that occurred if selecting sample
2) treats Epp top selection appropriately using epp conig parameters

1.Faster start of Epp when resuming a prior halted
2.Faster traversal of Epp gating hierarchy when resuming a build of Epp
3.Slight optimization by avoiding re-computing of Epp pairs when strategy is to always reuse a parameter
4.If Epp leaf has ZERO clusters than build using all inclusive rectangle manual gate for leaf subset … ignore outlier inclusion. Sigh.
5.In MDS match table allow user to see GatingTree position of highlighted rows
6.GatingTree search notices matched names of subsets

1)When relabeling FCS markers we MUST synchronize the GatingTreeTable
2)Slight improvement to contour visualization
3)Handle GatingTree selection properly when cancelling Epp
4)Label top of scale if T==10,000
5)If using parameters from GatingTree for Epp then do NOT use parameters of Epp parent
6)Better background color for progress bar
7)Improve tooltips for Epp top and Epp subset gates
8)Make row height of MDS table higher for seeing the superscripts on Epp gates
9)If not deployed allow user to switch to Bangalore grid which has many bugs
10)Handle manual gates … ESPECIALLY poorly drawn polygon gates

1)Epp configuration window is no longer modal which makes it easier to compare Epp runs
2)If Epp is cancelled selections for MDS are not made as it can lead to accidental deleting of everything
3)User can make GatingTree selections while Epp configuration window is up and use the parameters of those selections for Epp by clicking “Use GatingTree parameters” link at middle left of Epp configuration window
4)Show start time of Epp run in Epp top gate with tool tip hovering
5)Show duration of Epp run for Epp top gate with tool tip hovering

1)Allow legend for supervised UMAP subsets be a separate window with radio buttons. Clicking button highlights subset
2)Speed up Epp by using normal distribution grid from KlDivVectorized.

v 4.89
1)Support Epp’s minimum split parameter for 2D PathFinder when using separatrix scoring
2)Fix bug where changes to clustering made in the plot editor window that launched 2D PathFinder impairs the 2D PathFinder’s ability to synchronize that PlotEditor window when user clicks on a plot.
4)Support previous mis-interpretation of FCS keywords that caused AutoGaTe to treat Cytof files as non Cytof because the cytof_data_shift keyword was empty.
5)If Cytof data THEN improve W, A and T parameters of Logicle so that the plots look identical to FlowJo X plots for Cytof
6)Support Epp’s minimum split parameter for 2D PathFinder when using separatrix scoring
7)Make match identifier column of match table for MDS window a ranking of qf dissimilarity where 1 means #1 (top match)

v4.487 adds ability to do group expand of gating sub hierarchy with meta-click on MAC and ctrl-click on WINDOWS

1)General cleanup to handle 3rd type of separatrix score
2)Fix typo where boolean and was represented as bitwise and
3)Fix bug caused in visualization where non Epp gates get marked as EPP gates (YIKES)
4)If separatrix is best balance or best separation then kld criteria is hard stop
5)if separatrix is new 3rd type of best separation + kld then criteria works as test of separatrix in normal being 400% of actual distribution

1)Fix selecting bug where additive occurs if already selected despite the parameter asking for NO ADDITIVE
2)Consistent wording for tooltips and text of window managing from Figures.m
3)Ensure saved position of a manual gate is not LOST after the gate is saved ….

adds new type of separatrix too both Epp as well as 2D PathFinder

refines Epp by allowing the user to specify a minimum Kullback-Leibler divergence to rule out 2D projections that are not informative but are instead BLOBs.

1)Allow user to synchronize colors in current MDS display with subset highlight colors
2)Avoid MASSIVE tooltips in GatingTree when too many highllghters are active.
3)Provide right-click menu item in GatingTree to see overlap of ALL active highlithers for a sample into the current gate focussed on in GatingTree

increment for GenieWiki release

Ensures that user can not apply ZERO highlighting colors to MDS display and that applied colors can be made persistent.

fixes FATAL bug in 2D PathFinder caused by recent programming for UMAP visualization

1)Improves the “Use highlight colors” dialog box to report # of pre-selected highlight colors and to allow user to choose the default hue saturation ljghtness coloring
2)Shows the “Use highlight colors” the FIRST time a MDS match window is created to help remind the user

1)Allow opening PlotEditor window from SubsetHighlighter window
2)Ensure orphan gate is created under a grouping gate named “Orphan gates”

version 4.476
1)New features for sanity checking Epp and all gates
A)Orphan detection: ability to count and create gate for events OUTSIDE of a subset that have similar marker expression within % of standard deviation from marker means on subset
B)Ability to compute orphans and create their gates from 2 windows: a)1DPathFinder b)match table for ZMDS window
C)Ability to see coefficent of separation in match table for MDS window
2)Ability to open PlotEditor window from statistics table in MDS window
3)Ability to see and find QF match name for Epp subset in GatingTree window.

1)Continue improving the matching of clusters between original data set that created supervised UMAP template and the data set using the the template. DBM clustering is needed with some fairly smart stuff
2)Improve naming of template files when Epp top gate is used
3)Ensure that the SAME cluster analysis is done between Supervisors object for matching and the FcsTreeGater object WHEN the FcsTreeGater object is using very high. The cluster analysis for Supervisors object is only in effect in PlotEditor window for visual purposes but can be very confusing if the clusters do NOT line up.
4)Improve notification of multi-selection in effect on PlotEditor window since MatLab mis-reads the state of the command key and Ctrl key if focus changes to other windows outside of MatLab.
5)Fix new P2 bug when closing GatingTre that occurs ONLY if a ParameterReduction window had been open for TSNE/UMAP.
6)Make our Density-based Merging clustering open source since it is FULLY and COMPLETELY protected by patent and easy enough for any one else to implement by reading Darya’s latest description in the publication https://www.nature.com/articles/s42003-019-0467-6
7)Many cosmetic fixes

v4.474 Fixes string column alignment bug that causes wrong results with supervised UMAP when the applied to data FIRST does not have the correct column order.

1)If TSNE/UMAP is in PlotEditor then pay attention to a concurrent change to the current map made by a separate ParameterReduction window.
2)When applying a template that is created with supervision of Epp or non Epp gates, MATCH the applied-to embedding to the original embedding using simple medians of the supervised gates.
3)Copy the original supervised templates gate colors and names to the matched UMAP islands in the applied-to embedding
4)When looking at a UMAP map that is created by a supervised umap show the legends for the original template’s highlighting and names in both PlotEditor and ParameterReduction windows.
5)Allow user to turn ON/OFF the supervised UMAP template’s color highlighting and gating when the user clicks the Highlight button in either the PlotEditor or the ParameterReduction windows.
6)Support sort order variation in SubsetHighlighter window

V4.472 Improvements to UMAP templates
1)If template data is subset of data for new umap then allow reduction of data and ask user if this is okay
2)When using template use the same plot scales as the original umap reduction that created the template
3)Initial logic for cell true counts which is based on mixing beads and cells

1)adds supervised UMAP examples for MathWorks FileExchange
2) improves legend for highlighting in run_umap as well as in Tsne.m so that clicking on legend elements causes them to flash in plot display
3) removes error-prone duplication of files in matlabsrc and matlabsrc/umap/util by moving duplicates to matlabsrc/util

v4.470 keeps used file identifier separate from current file identifier in parameter reduction (Tsne.m)

1)Make it easier to synchronize MDS default colors with highlighter colors chosen by user
2)If invoking parameter reduction on Epp gate always use Epp parameters
3)Cosmetic cleanup after demonstrations at Cyto 2019
4)Always allow supervised UMAP if NOT merging other samples

v4.468 Ensure that parameter reduction from MDS window selects Epp parameters

Changes at Cyto 2019 first 2 days
1)If first time in PlotEditor then don’t ask user
2)Allow MDS window to activate ParameterReduction in either PlotEditor or ParameterReduction window

1)When user closes GatingTree window with open parameter configuration windows but HIDDEN ploteditor associate windows …. make sure that the hidden ploteditor window is not restored next time the GatingTree is open.
2)When use selects Hi->2 toolbar button do not complain if there are inelligble selections in the GatingTree

Put direct links to cytogenie.org in GatingTree and ParameterReduction windows

1)Embeds links to GenieWiki using easier-to-read static method “setHelp” in CytoGate.m
2)Supports Connor’s new programming for supervised UMAP
3)Ensures that UMAP template processing does NOT require same channel order but ONLY requires
A) Same # of parameters between training set (template) and test set (current data)
B) Compatible marker names for all parameters or all except one parameter with empty name (only one) FMO

Follow project convention of wrapping in MatLab classes all cryptic calls to JAVA static procedures to
a) make it easier and briefer to read.
b) minimize typing ererors

provides enhancements to address 2 issues that occur when user changes the visual scale of a parameter to an extent that radically differs from the scale reported by the instrument through FCS keywords
1) The clustering in such cases was not accurate or useful.
2) The gate labels were drawn off the screen. Can’t be seen.
These are greatly improved.
Fix problems with new feature to synchronize density scales to large visual scale changes
1)Property for scale change was being remembered GLOBALLY which could hurt on related experiments
2)When changing scale BEFORE any gates made AutoGate would TRANSPOSE the axes visually which is VERY annoying

1)Supports wider data scales for samples like Esmond’s where the upper end can be higher than 10^7.
2)Make it possible to narrow the visual limit down to 3 standard deviation units above the mean.

1)provide improvements & bug fixes found when creating tutorial for UMAP

1)Do not retain cancelled UMAP if it is less then 1/3 of its epochs formed
2)Allow user to continue UMAP if they ACCIDENTALLY clicked cancel on progress bar
3)Clean up and stop UMAP if user closes ParameterReduction window during UMAP processing say YES to halting parameter reduction.
4)Ensure when using probability binning at start or during UMAP that at least 8192 bins are used and no less than 4 events per bin

1)Fix MAJOR bug in saving UMAP template
2)Fix FATAL exception when running UMAP if user uses parameters that are uncompensated or linear side scatter or logicle forward scatter
3)Allow user’s with Python to choose Leland McInnes implementation

improves wording and information during UMAP generation … MOREOVER v4.457 allows user to KEEP an incomplete UMAP if they click CANCEL

1)Ensure it is easy to dismiss the ParameterReduction window AFTER a user has clicked CANCEL on a UMAP run
2)Improvements to workflow for UMAP template saving etc

now displays pgoress of UMAP processing in plots and allows user to cancel.

v 4.454
1)fixes a BUG found by Connor in my JAVA code (which may lead to an improvement in the algorithm by accident)
2)Allow user to save and re-load UMAP results to/from their file system as templates for incremental embedding

1)Deprecate Leland McInness implementation of UMAP
2)Remove need for Python installation
3)Use Connor Meehan’s MatLab implementation which includes FASTER incremental embedding feature for multiple samples. FlowJo does not have this incremental embedding.

v4.452 improves activating heat map DIRECTLY from GatingTree by supporting
1) unique tool bar button for activating on GatingTree tool bar
2) ANY combination of GatingTree selections

1)Fix bug found with BIolegend Titration by Brissy where exception occurs if applying manual gates that find ZERO events/cells
2)Make deleting always focus on the gates associated with GatingTree selections
2) Allow heat map to be called DIRECTLY from the gating tree on gates associated with GatingTree selections from the HiD window menu and Hi->2 toolbar button. Keyboard acceleartor is alt-E

1)Fixes FATAL exception when saving a gate that is a NOT gate or Epp top gate. This was introduced 4 days ago
2)Display correctly when user uses html characters like <hr> in the gate name or sample name
3)Display correctly when user uses latex characters like ^{superscript} in the gate name or sample name

1)Fix PlotEditor display problems introduced by new code in v4.448
2)Handle scenario when user CANCELS the UMAP external python process

1)When opening PlotEditor show bigger version of GatingTree gate image and announce whether gate open on parent cells or on gated cells
2)Fix bug of refreshing prior figure after pop up when the figure is INVISIBLE. Make sure that the dummy dbm_gui (PlotEditor) window is in fact deleted after main.m starts

1)Whether choosing a sample node or gate node in the GatingTree for MDS display, always ensure that the first choice is on the left plot and the 2nd choice on the right plot of the MDS window. Previously left/right plot order and GatingTree choice order only worked if BOTH choices were gate nodes. Not sample nodes.

2)When activating flashlight dialog from MDS window or from phenogram window give the user the choice to copy each subset’s MDS or phenogram color to that subset’s highlighter color IF the highlighter color was previously NOT set.

1.Fix subset labels in PlotEditor window so that Tex characters like “_” (the underscore character) do not distort the labels.
2.In PlotEditor window provide new menu item that allows user to override the first X and Y default parameters for a staining panel
3.When cells in PlotEditor are parameter reduced or Epp top menu support using default X and Y parameters AFTER user restricts plot to any cells within a gate (clicks down arrow at bottom right)
4.If gate is Epp gate or NOT gate then provide a text object on the XY plot visualization to remind users of the special nature of the 2D projection.
5.Allow user to activate the 1D PathFinder window from toolbar of the MDS sort table window …. for each of the selected rows in the table.
6.Allow user to activate the window manager menu from toolbar of the MDS sort table window ….

1)Do not loose the qf property files when exporting meta data as an AGI file or copying .autoGate folder. The qf property file is produced by the HiD match process which can be expensive time-wise to re-create.
2)If Time is NOT an FCS parameter, then use event # FCS parameter for BOTH parameter reduction as well as for Epp. Moveover, avoid event # FCS parameter if it has only one unique value and is corrupt. This was found with some samples in Holden Mecker’s CyTOF publication of 2018
Allow user to activate MDS, parameter reduction or phenograms when selecting at the GatingTree level of SAMPLE type.

1) Support X and Y axis positioning when drawing manual gate
2) Allow user preference setting for order of axis labels when generating a new gate name
3) Deal with 1D histogram gates when reporting overlap into gates from highlighting gates
4) Defend against major exceptions in democratic W and AutoComp setup wizard with CyTOF files for Holden Maecker’s 6 center publication

cosmetic improvements to Parameter reduction

1) Change GUI semantics of 2 parameter reduction options to “Open parameter reduction in PlotEditor” and “Configure parameter reduction. NO MORE probability binning language.
2)If open in ploteditor parameter reduction is for specific choices ensure prior exists or redo.
3)fixes no cluster borders in v4.441 ParameterReduction window because CVS commit was not done

supports probability coloring (pseudocolor) and cluster density detail control on ParameterReduction window

Bug fixes and improvements found with Connor when preparing for lab meeting on UMAP for April 8, 2019

1) Use Epp match name in highlighter list descriptions
2) With Epp matched names put Epp name after matched name
3) Ensure F & QF scores are shown as percentages
4)Fix bugs with Pbe
5)Make sure Epp-matched name is seen in highlighting legend

1)Fixes issues in new (8 days old) sort table for MDS window when clicking on toolbar buttons for gate sequence and highlighting when unmatched subsets are HIDDEN on the parent MDS window
2)Allow user to see highlight overlaps into the current cells displayed by the PlotEditor window

1)Fixes bugs in gating parameter reduction output caused by democratic W changes 9 months ago and recent UMAP addition to parameter reduction along with tSNE
2)Removes row filtering from MDS sort table
3)Adds highlighting and comic strip (gating sequences) to toolbar of MDS sort table

1)In the MDS window in the new sortable table describing matches
a)Allow user to reorder columns as well as rows (SORTING)
b)Ensure that the html and excel exporting of is AWARE of user reordering of either columns or rows and the FILTERING of rows
c)Ensure that selecting rows to cause symbol flashing in the MDS graph is sensitive to the reordering of rows and columns and FILTERING of rows
2)In the MDS window support a toolbar button that allows user to create html for the heat map, the MDS graph and the sortable table of matches. And ensure the html can be easily zipped and moved by arranging images in sub folders.
3)In the MDS and Phenogram window support better mouse operations on HEATMAP so that click on name column causes flashing of graph symbol and so that hovering only produces noisy tooltip on the name column. Hovering on measurement columns causes reporting of measurement expression at bottom of window and NOT tooltips.

allows user to see summary table of matches from MDS window toolbar. Table is sortable and exportable to Excel

Puts buttonss in conventional locations for ParameterReduction window so that the bottom right (south east) corner holds the main actions which run the parameter reduction and use it thus closing the window.

Update under construction messages and fix bugs in new parameter reduction

1)Clean up display for parameter reduction in plot editor window with checkboxes to see contours or DBM clusters
2)For many pins do not turn ON/OF glass pane infinite progress genie so many times. Sigh.
3)Support calling parameter reduction window from GatingTree, not just probability bin embedding
4)If algorithm is UMAP than the max iterations GUI element on “Parameter reduction window” is used instead for min_dist input for UMAP. Support gray colors if cell highlighting is active.

V4.431 is first version with support for UMAP ( uniform manifold projection).
It invokes the Python implementation and guides the user to the correct installation with python.

supports Darya’s new requirement to allow user to vary the SDU threshold for scatter (and stain) parameters
Support invoking uniform manifold projection in original Python implementation.

implements latest new requirements for quality of match precheck

lets user choose BOTH type of data as well as type of standard deviation when computing quality of match logic.

1)runs quality of match deviations on logicle data not compensated
2)allows user choice of normal standard devaiation or robust. Removes v4.426 choice of overlap
allows user to choose normal standard deviation versus robust (MatLab’s std versus mad). The default is mad since std is weaker and less discriminating than mad for subset overlap

It is now possible with samples both large in frequency (>3 million) and parameters (28 colors, 6 scatter) to do the comparison despite the inefficient match merging logic.
1)We can limit the # of mergers per subset by saying <= a # of matches. Those discarded are prioritized
A)If the comparison is for same sample, then those discarded are those with lowest overlap to the subset being compared to
B)If the comparison is for different samples, then those discarded are those with highest QF (most dissimilarity) to the subset being compared to
2)It is possible BEFORE the painful merging process begins to refine which subsets to ignore.

1) Fix problem with NOT gates when “Gate label preferences” is “Use legend” as with Justin’s TReg experiment
2) Improve toolbars on PlotEditor and GatingTree window

is necessary because unpredictable disaster can occur if when ijmporting an analysis the GatingTree has either of these states
1) It is currently open
2) It was previously using a different compensation or logicle transformation

1)Rewrite of democratic W so that samples with different channel layouts in same comp matrix identified by stainSets.properties can be processed.
2)AutoGate setup ignores channels whose label begins with “sampleid” or “ratio”
3)Support for large keyword values in samples like those in the published omip T cell experiment.
OMIP-044: 28-Color Immunophenotyping of the Human Dendritic Cell Compartment
Florian Mair,* Martin Prlic*

1) SubsetHighlighter uses MDS frequency and colored symbol for match color .
2) Double click activates SubsetHighlighter in both phenogram and MDS window when MORE than 1 subset is selected
3) On 1-click popup menu for MDS window the hints in menu item suffixes for mouse/keyboard accelerator gestures are now CORRECT
4) Phenogram & MDS overall are more consistent with tool tips, with 1-click menus plus their mouse/keyboard accelerators. Phenogram differs in selection behavior.
Remove confusion of 2 questions from the “Do you want to exit” query of the main window.

continues improvements to highlighting from phenogram with new modeless (non modal) pick window

1)Minor defects and incomplete things in the new features of v4.418
2)SubsetHighlighter window that is non modal and allows recoloring and highlighting instantly or by refresh. a)Activates from click menu of MDS or Phenogram
b)Additional features for GatingSequence window: highlighting with auto-refresh or manual refresh
3)Issues for Microsoft Windows for high definition monitor. Had not tested Microsoft Windows in 3 weeks

1)Support launch of easier highlighting window SubsetHighlithter from MDS and Phenogram and Tsne/Pbe windows for HiD analysis. Window is new NON-MODAL or modeless dialog window “SubsetHighter” for turning highlighting ON/OFF or re-coloring highlighting WITHOUT closing
2) Support Gating Sequence window “hearing” changes to highlighting and EITHER having a refresh button or “always refresh” button.
3) Support cascade/toFont/close of GatingSequence and SubsetHighlither windows from the windows management menu of GatingTree window or on W toolbar button other

1)Add feature to clear HiD selection history
2)Improve menu wording for HiD selection history and make popup menu match window menu match toolbar tooltips etc.
3)Assist/guide user to expand single GatingTree selection to 2 selections for HiD matching of Epp to non Epp regardless of whether the selection is Epp or non Epp gate
4)Assist/guide user to expand single GatingTree selection to 2 selections for HiD matching of Epp to non Epp regardless of whether the selection is Epp or non Epp gate
5)Improve wording of Gui that guides user expand 1 gate selection to 2 for HiD matching
6)Better wording on progress window to guide the user to speeding up HiD matching during merging.
7)Improve menus and error messaging for HiD operations

1)Allow the module invoker to disable the choices
2)Improve GUI for analysis management. Add new feature to rename an analysis

1)improves label transparency on PlotEditor
2)Let live singlets be gated with 1 menu item on PlotEditor

1)Improve management of 1D PathFinders that are associatec with a MDS or a Phenogram window
2)Allow 4 levels of subset info detail for tool tips on HiD Phenogram and MDS views
3)Add HiD selection history menu items to JAVA menu on HiD toolbar button of GatingTree

improves prevention of running out of memory by providing slower JAVA implementation of QF that does not vectorize the operation. So it is slower but it works.
Color changing is allowed on click popup menu of MDS window
Manage tool tips better

prevents running out of memory by providing slower JAVA implementation of QF that does not vectorize the operation. So it is slower but it works.
Epp also is 5-10% faster

1)Constantly do memory cleanup while running Epp to eliminate temporary gates.
2) Make sure parent Epp node always has Epp timing associated with it which did not happen when first split had no further splits with Shanel 4 million nasal tissue cells.
3)Fix problems observed when using 2 physical monitors

1)Deals better with the risk of too many probability bins running out of memory during QF Match
2)Handle deleted gates in selection history and notify user where they are in history after clicking prev or next
3)Allow windows to be managed from toolbar on PlotEditor, Phenogram and MDS windows

This introduces 2 new productivity features suggested by Wayne Moore this week on Jan 17, 2019 to aid HiD research:
1)Allow user to close or see all windows related to an experiment.
2)Allow user to go to prev/next GatingTree selections that were made for or from a HiD View (MDS, Phenogram). This comes complete with keyboard accelerator (meta-left or meta-right) and toolbar buttons on menu items on HiD menu of GatingTree window

1)Fix bug WHERE adding/removing new subsets to a gate sub-hierarchy does not get reflected in phenogram IF the phenogram for the same sub hierarchy was previously created. The user must reset the cache for the experiment to see any changes.
2)ON phenogram window provide selection, mouse click, motion, tip and popup menu improvements
3)Always give user a chance to see even only 1 subset’s gating sequence in the browser with constrained table columns

1)Give user a chance to continue with QF match when out-of-memory by ignoring LARGE clusters
2)Make tSNE plot support gray scale for better highlighting
3) Alter comic strip by putting leaf gate’s 1D PathFinder first

1)Remember computation cost times at right corner of MDS window and Phenogram window
2)Better icons
3)bug fixes

improvements to icons and wording of HiD methods based on feedback from Lee

makes cosmetic and wording changes to HiD/NTo2d operations so that Pbe is more visible and Epp is known to be ALWAYS the first necessary step to AutoGate HiD benefits

1)Fix bug in previous AutoGate workflow of applying semi-supervised or supervised gate hierarchies to avoid java null pointer exception when no clusters are found by DBM and no gate is found
2)Further perfecting of normalizing scatter parameters to be used alongside of logicle parameters by Follow Connor’s advice for handling log10 conversion of 0 or negative numbers so that they fit in a region below the lowest positive number if it is less than 1 and otherwise fitting it between 0 and 1

1)Fix bug created about 6 weeks ago that prevents user from seeing high res 1D PathFinder with all parameters when there are matching parameters.
2)If left and plot are the SAME cells then do NOT ask “Which plot left or right” when user clicks “See events” link on MDS display’s toolbar.
3)Prevent zero from log10 calculation which produces INFINITY

fix to the infinite loop has created another bug that only occurs with data like OMIP where scatter channels have negative values. Not sure why I did not think of this “edge” data case in 2018.

1)Fixes various data processing issues exposed by OMIP dataset for B cells found in Cytometry
2)Makes it easier to turn off annoying tool tips in Phenogram and MDS windows by putting checkbox in tool tip.

1)continues fixing mutli-monitor positioning problem with MAC OS High Sierra or later
2)avoids bug caused with probability binning
3)Makes “See events” look & feel similar to “See phenograms”
4)Provides progress bar for “See phenograms”

1)Allows user to toggle between choosing from selected subsets versus ALL subsets
2)Fix multi-screen issue found on some versions of MAC OS X

1)Ensures that with ONE CLICK you can turn on or off the highlighting (i.e. back-gating) of MULTIPLE subsets from the Phenogram window
2)Fixes bugs with latest Pbe (probability bin embedding) based on tSNE which is launchable from N2D views of MDS and Phenogram

1)Ensures Pbe feature’s window comes up more smoothly from MDS display
2)Support Pbe feature in Phenogram along with easy highlighting toggling

1)Fix 17 month old problem with tSNE where the scatter variables are not “normalized” using the Log10 idea of Wayne Moore
2)Make it easy for user to toggle highlighting ON and OFF by clicking on the symbols in the MDS display

improves Pbe

introduces new feature “Probability bin embedding” which is tSNE with probability binning which makes subset separation less crowded and makes tSNE faster and makes it reproducible.

Introduces a new feature asked for at Dec 17, 2018 lab meeting for showing degree of match similarity with heat map colors based on earth-mover’s distance…this helps see quickly degree of difference in one glance. One activates this from the EMD toolbar button on the MDS display.

adds to heat map:
1) Legend to describe marker expression
2) Column for frequency

provides heat map column headers rotated 45 degrees in major commercial browsers (google chrome, safari and edge)

Fixes bugs related to the new GUI for Epp and MDS and phenogram

makes heatmap tool tips better

1)Support vertical labels for markers in heat map
2)Don’t show scatter in heat map
3)Handle larger phenograms >25 subsets