Gene View can now be selected and filtered in the top left hand corner of the Graph Window. This allows researchers to focus only on parameters of interest when gating in Gene View. PCA now contains options to normalize and log transform parameters used for the dimensionality reduction, greatly improving the resulting clustering.
Release notification mechanism to let users know when the next release becomes available. Active for releases post SeqGeq v1. If you have any questions or comments regarding the SeqGeq platform we greatly appreciate any feedback.
October 13th , Version 8. July 5th , Version 8. Copying layouts between workspaces crashes. May 17th , Version 8. May 4th , Version 8. April 28th , Version 8. April 3rd , Version 8. Does not support OS9. Minimum version is OSX.
Minimum workspace readable is version 20 2. For old Workspace, read using version 6. April 13rd , Version 6. November 16th , Version 6. September 30th , Version 6. The format of the workspace file has changed. Workspaces saved in 6. September 10th , Version 6. Workspaces saved in FlowJo v6. July 5th , Version 6. Autogate tool. Point… click… gate. Choose the new autogating tool in the graph window, or simply hold down ctrl-option as you move the mouse over any bivariate graphic.
Note: if you hold down the mouse button as you click to create the gate, you can then track the mouse to inflate or deflate the gate to size it with even more precision! The SciBook is a place where you can store pictures, text, tables, or custom annotations. The SciBook is stored with the workspace; you can use it as a permanent record of your analyses, as a temporary holding place for outputs, or just to keep notes for yourself. Contents in the SciBook do not change-therefore, if you change a gate, delete a sample, or make other modifications, the SciBook contents will not be modified.
Once in the SciBook, you can copy into other programs, print, or simply just view. The SciBook gives you an interface to add comments about each item that you insert, and records the date and time that the item was inserted. The SciBook is meant to evolve; we look forward to your comments regarding which features you use the most, what features you would like to see in the future, and what you do and don't like about it!
Backgating Analysis. Validating gate positions is one of the most important aspects of multiparameter Flow Cytometry. FlowJo now provides you with a tool to view the effect of every gate on your final gated population! FlowJo shows you a window where each level in the gating hierarchy is displayed, with the final gated population overlaid at each level.
Therefore, you can quickly scan to see if any one of your gates is positioned incorrectly. The backgating display can be printed, copied, or saved in the SciBook see below. Boolean gates. You can now create a gate which is a Boolean combination of any existing gates i. Boolean gates are "live", meaning that they will reflect any changes to the gates on which they depend.
FlowJo can also automatically create a series of Boolean gates that represent all combinations plus and minus of a set of gates. For example, if you have a sample which was stained on different parameters for IL2, TNF, and IFNg, you can create a positive gate for each of the three cytokines for example, a histogram gate. Then use FlowJo's Boolean Combination to create the 8 gates that represent all combinations of expression of the cytokines e.
To create or edit Boolean gates, choose the parent subset s and select the menu item "Boolean gates Derived parameters. You may now create a derived computed parameter that is any algebraic combination of existing parameters. FlowJo allows you to specify arbitrarily complex formulas, and includes a wide variety of mathematical functions that you can use to transform the data.
This platform can be used in FRET calculations to create a parameter that reflects the efficiency of resonance energy transfer.
Layout Editor: New Statistics Table. FlowJo now renders tables of statistics in a beautiful and highly customizable way in the Layout Editor. You can copy tables either by dragging them from the Table Template Editor to use with Batch iteration, or directly from a completed table.
Or, you can create them from scratch, adding your own statistics and keywords and other information. Statistics Tables in the Layout Editor come in two flavors: 1 Each row is from a single sample: this is like the output of the table editor, where statistics for subsets or the whole sample are all represented on the same row; 2 Each row can have subsets from the same sample: this allows you to view a number of statistics e.
Note that you can copy Layout Statistics Tables directly to spreadsheets as tabular data or to graphics programs as their graphical representation. Layout Editor: Overlay legends. The legends for overlays in the Layout Editor can now be customized to show statistics, keywords, or other pertinent information from each subset that is overlayed in the graphic.
Simply double click on the legend to specify what should be shown. Layout Editor: Iterate by "nth" sample. Sometimes you just want to do batch iteration where the order in which you collected the samples defines how you want the output to appear-for example, every three tubes comes from a single sample, where the first of the three is a control, and the other two are two different panels. FlowJo lets you easily specify such a design by using the "Iterate by nth" option.
Choose "Iteration options" under the layout menu. In this example, you would iterate by "every 3rd sample", telling FlowJo to group tubes into samples of 3. This significantly simplifies batch operations. Templates : Improved functionality. This "Iterate by nth" Layout Editor feature also means that Template Workspaces that contain batched layouts will work well. A batched layout is now automatically defined to have the appropriate iterator and discriminator values; when you batch a layout over every sample and save it as a new layout, the new layout is automatically defined to iterate by "nth", where "n" is the number of tubes in the original batch.
In addition, sample identification is significantly improved in FlowJo. This means that Template workspaces will fill out layout graphs as expected-FlowJo tries very hard to overcome any ambiguities that might arise because of multiple samples fitting the criterion for a single graphic.
Current Version is 9. Index: Version 9. Decreased memory requirements. Together, these two improvements allow tSNE to be run on one million events with 12 parameters! Note that this can take two hours on a laptop. Can also initialize from previously-added PCA parameters-this means you can compute PCA on a predicate sample, copy the PCA vectors to other samples, and initialize SNEe on those identically-computed vectors for greater cross-sample similarity. Parameters v9. But when you concatenated files and add a keyword as a new parameter, it assumed this was an uncompensated parameter and didn't show it.
New concatenated files add a notation that this parameter should be shown in menus. Compensation Spectral compensation UI: Minor updates. Access is similar to the Y by Y platform select a single graphic and choose Y by Y from the menu or the contextual menu. Select parameters-FlowJo will create a copy of the selected plot with every pair of the selected parameters controlling color in a polychromatic plot. This tool is useful for exploring a tSNE plot for expression and co-expression of markers-a single click to get tons of info.
Removed limit of 50 overlays in a single Layout graph item. Fix: Reducing dimensions of an LE table containing objects doesn't crash. Fix: Copying or pasting a textbox in the Layout Editor preserves all styling information. Fixes Fix table outputs : Reduce double commas in gate names to one. Fix: Minor UI bugs in the custom transformation editor dialog. Implement smart sorting of groups, tables, and layouts in menus and lists.
Fix: Prevent crash if PCA platform shows only one parameter. FlowJo v9 Manual. FlowJo now creates graphics as PDF format. By default, whenever a graphic is copied, the PDF format is also put on the clipboard. This makes for high-resolution graphs when pasting into PowerPoint and other programs. You can also include SVG for programs like Intaglio. In general, most programs will select from these multiple formats the one which is best for them; however, if you find this is not the case, you can change the preferences to not include PDF or SVG.
You can also choose to save a graphic as a PDF file by preferences. When you do so, the entire graphic will appear as on a single page with no headers or footers. If you want pagination and headers and footers, then simply Print your graphic, and from the Print dialog, choose "Save As PDF" rather than printing to your printer.
A few rare fonts including "Symbol" will not appear properly in PDF outputs. If you find this to be the case, choose a different font in FlowJo. Minor changes: Workspaces can now be sorted on the basis of the Disk Filename i. Create Group dialog will identify all unique stain combinations, no matter how complex Minor bug fixes Aug 27th , Version 9. General bug fixes April 26th , Version 9.
This statistic normalizes the RMSD by the number of events, providing a value that can be compared across samples with different event numbers. The SSM provides a direct indication of which combinations of fluorochromes result in lower sensitivity from spillover spreading.
Higher values in the SSM show spillovers that will reduce sensitivity more than lower values. Export dialog now show stain names when possible Bug fixes: Fix an error that occurred rarely after dragging gates from one workspace to another. Bug fixes: Various stability fixes November 16th , Version 9. Complex layouts batched to a new layout will suggest using Preview as output A number of bug fixes aimed at improving performance September 19th , Version 9.
As usual, however, you can save a workspace as XML and open that in older versions. New Features: Parameter lists in layout "multi item edit dialog" are now sorted according to preferences Workspaces with large numbers of keywords operate much more efficiently Better refresh on some dialog windows when resizing New PREF for cyTOF files that allows setting uniform range for all parameters.
Used for CyTOF files to set uniform range for all parms You can use this to determine appropriate ranges for thresholds for failures. Fixes bug introduced into 9. Option-clicking on a workspace header will sort by that keyword and add it to the sort definition so you can option-click on successive column headers to do a complex sort.
Don't highlight enable transformation menus for uncompensated samples Allow different transformations for uncompensated parameters with different ranges Important for CyTOF files Allow reading and skipping layouts that are corrupted and read other layouts that have not been affected Comparison Node: Leave enough space to display Overton Percent Positive value. Boolean gates that refer to gates that have "G " in their names like " gate" are properly shown in the display window when they are edited Multigraph overlay accommodates larger axis text from prefs Moving multiple objects within grids preserves order July 27th , Version 9.
Compensation Wizard better handles samples with off-scale scatter measurements. New Preference on the General tab to turn off sub-channel randomization of measurements during compensation - makes picket fencing happen but prevents small changes in membership of gated events on compensated parameters. Population Comparison: Overton statistics added to Layout Editor annotation box. Boolean gates that refer to missing nodes now show "RefError" in the Workspace statistic display.
Added "? Compensation Wizard will use your custom scatter gate if you have pre-defined one. This is a menu item-- creates a new "shell" group that has all the gates and information from the previous group, but no samples unless samples are auto-added. Similar to a template, but for groups. Can be workspace-specific. Note: this preference may apply only to samples added to the workspace afterwards Bug fixes: Layout item information dialog disables the foreground color selector on overlays, since that didn't do anything; disables the "show all layers' gates" checkbox when it's not an overlay.
Fix rare crash on reading remote FTP data files. Ancestry plots from Layout Editor are not clipped when copied and pasted into PowerPoint before ungrouping. Site license access made more robust in case of server issues.
Allow dragging gates onto comparison nodes to change control Deleting a derived parameter will not cause an exception when reopening graph that showed that DP Export non-FCS format bug introduced in 8.
The workspace comment column text is properly added to Layout Editor Tables. The Group Editor dialog window doesn't show funky characters for empty parameter stain names. The Kinetics smoothing options are properly initialized in the kinetics window when re-opened.
When reading DiVa 3. Templates with layout editor iteration that depends on keyword iteration and discrimination now work fully. Templates no longer give the error that the file was not properly closed. Allow CellQuest data files with zero events to be added to a workspace. Group Edit Dialog window properly initializes the comparator menu item.
In Layout Editor Tables that have a column for "Gate Name" -- for sample-level nodes, the sample name is shown instead of the text "Ungated. There are new UI checkboxes in the overlay information dialog to set this. Layout Editor Tables can show the gate name with an "indented" option -- to make it look like the Workspace display. When creating a new Layout Editor Table, you can select from the popup menu an option to create a table that looks like the current Workspace as much as possible ; it automatically creates the appropriate columns.
When you "concatenate" samples or gates, you can now choose to create new parameters in the resulting data file, the contents of which are equal to keyword values from each of the samples. Use the option-key when selecting "concatenate" from the menu.
This let's you add identifier information or other information found in the keywords as a real parameter, on which you can gate, etc.. Empty workspaces show "Drag Samples Here" text. When you drag a population onto a layout graph to create an overlay or hold down cmd-key to reassign the graphic to that population , FlowJo will now replicate that operation to ALL layout graphs that are currently selected.
Added Concatenate User Interface link. All recalculations are now done "lazily" -- when needed. Fixed Group Edit dialog. It now remembers all comparator states "does not contain" etc properly. Your serial number will transfer and automatically authenticate all versions of v Your dongle will automatically authenticate all versions of v9 and v Your serial number will transfer and automatically authenticate all versions of v9 and v Upgrade to v10 with your existing dongle: Contact Sales.
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