These are the latest features added to WinList.
This is a minor version update with many new features and enhancements.
It is a free download update for registered users of WinList 7.0.
See the Highlights and License Options pages for additional details.
WinList now uses additional threads to improve processing performance.
A Miscellaneous preference has been added to enable/disable the use of threading. By default the "Threading" preference is enabled to improve performance. On computers with limited resources, you may need to disable threading.
The "Undo" command has been added to the Edit menu, with keyboard shortcut Ctrl+Z. Undoable actions: region deletion, moving and sizing editing histograms, changing parameters, and editing graphics.
Time parameter improvements: WinList now detects the "Time" parameter and sets it for auto-zooming. It also converts the axis into seconds if the data file contains the $TIMESTEP keyword. The Time parameter is also set to "Auto-zoom" by default.
WinList is now "large address aware", supporting greater than 2GB of memory space.
MultiGraph printing now takes advantage of some of the printing options for Reports. If "Fast Printing" is enabled for Reporting preferences, MultiGraphs will use the "Print Quality" report preference and printing can be significantly faster on some printers.
MultiGraphs can now be saved as PDF files. Choosing File->Save->Save MultiGraph PDF will display the Export to PDF dialog, allowing you to navigate to a location and enter a file name.
Improved region deletion behavior: When a region is deleted, WinList now keeps track of all its properties and vertices, as well as the histogram it was originally created in. The region can only be redrawn in the same histogram, unless the Edit Regions dialog is used to "Clear" the deleted region. The Edit Regions dialog allows the region to be restored after deletion. When the region is redrawn after deletion, its original properties are maintained. These changes provide more consistency in gate expressions that reference the region, as well as providing a means for undoing a region deletion.
Holding the Shift key down when deleting a region will disassociate the region from the histogram so that it can be redrawn in another histogram. If the Shift key is not down, the deleted region remains associated with the histogram and will only be redraw in that histogram.
A region preference has been added to control whether WinList associates regions with the histograms in which they are originally created. The default value for the "Associate with Histograms" is enabled, which means that a region will only be redrawn in the histogram where it was originally drawn. Disable the property to allow a deleted region to be redrawn in any histogram. You can also press the Shift key when deleting a region to disassociate it from the histogram, even if the property is enabled.
NStat regions no longer limit rows and columns as a function of histogram resolution.
A Region preference has been added for the display option for NStat region labels so that it can be set separately from other region default label options.
A gate equation can now refer to other gates. For example, if G2=R1&R2 and G3=R3&R4, we could define G4=G2|G3. This would be equivalent to G4=(R1&R2)|(R3&R4). A gate can only reference gates that are defined ahead of it in the gate list.
A notification window now appears when a sort region is moved, sized, or deleted. The notification window can be clicked to edit the sort. The user can continue to work when the window appears; the window will close automatically.
When the Edit Gates dialog Reset All button is clicked, the program now resets the histogram gates to "Ungated" in addition to resetting the gate expressions.
The Edit Program Controls dialog will now increase or decrease the number of gates and regions for each data source if these values are edited. Previous versions only increased the number.
The Context menu for 2P regions now includes a "Conform to Other Regions" command. This command adjusts the current region so that any of its vertices inside of other regions are removed, and any vertices of other regions inside of it are added.
Edit Graphics dialogs now have an Apply button.
Histogram titles now update when a new file is loaded and when different parameters are selected for the histogram.
When the mouse hovers over a histogram title bar, a tooltip is now displayed to show the title bar text.
Default 2p graphic preferences have been modified to show Dots with Contour lines. This change will have no effect if you have already set 2p graphic preferences.
The Save Graphic command for histograms now supports JPEG, PNG, TIFF, and GIF formats, along with bitmap and metafile formats.
Contour drawing has been revised to provide improved graphics even with low event counts.
The 3D viewer has been enhanced. It now allows up to 1,000,000 spheres/dots. The user can choose the location for the axes, and there is an option to display the exponent only on the axis tics.
Histogram names now use the actual parameter names by default, instead of P1, P2, etc. Pre-existing protocols will use the same names they were saved with.
WinList now handles situations where the User Documents folder has been redirected to a network location. Registration information is now stored in a machine-specific section of the preferences file (WinList3D.INI). The program will automatically move existing information to the new section.
WinList now disables compensation if a new file is opened and its parameter resolutions differ from those that were used to set up the compensation.
WinList now quietly alerts users if Log Bias is turned on in a protocol. The alert offers to turn off log bias for the user.
Logic has been added to read FlowJo data files that do not conform to FCS standards for specifying data offsets.
The Transform dialog now supports Auto-zoom using several methods. With "Auto-Zoom to highest used channel" the program will automatically zoom to exclude empty channels at the upper end of the selected parameter. With "Auto-Zoom to Fixed Upper Boundary", you can specify a specific channel that will be used as the upper boundary for the parameter. And with "Auto-Zoom to Percentile", you can enter a percentile at which to set the upper boundary.
Quantitation has been revised and improved. WinList now supports quantitation on linear parameters, quantitation with HyperLog axis, and using slopes & intercepts derived from linear data. The Quantitation dialog (Edit Data Source) has been revised to improve efficiency.
WinList now ensures that its packet size is at least 200K events when it starts up with iCyt support. When starting up without iCyt support, the default packet size is 50K events.
Mousewheel scrolling in dialogs has been improved.
File Open and Save dialogs now use the native OS dialogs. The one exception is the File dialog displayed when adding files to the batch list, which cannot use the OS dialogs because it must be displayed at the same time as the Batch dialog.
When WinList is set to "autocompensation" files from keywords, it turns off compensation when it sees an identity crossover matrix (i.e. a matrix that specifies no compensation). Starting with this build, it also clears the compensation matrix in this condition.
When running on WinXP, the older XP-style choose folder dialog is used to pick a folder location.
The Preferences dialog now has a "Save preferences" checkbox on the page that allows opening of preferences from disk. Enable this option to make the newly opened preferences permanent.
A change has been made to the Save Data Source command. If the name of a parameter has been edited in the Names and Resolutions dialog, WinList will use that name as the $PnS keyword value if the file is resaved using the Save Data Source command. The original $PnS value is stored as PnAlias.
When the Open Macro command is used, WL now asks if you would like to run the macro you have just opened.
A "DDE Timeout" setting has been added to Miscellaneous preferences to control the amount of time (milliseconds) that WinList will wait for a remote script command to complete. The default setting is 10000.
WinList now creates a $TIMESTEP keyword that allows conversion of the Time parameter to seconds
If a HAPS had two features with the same name and they were both selected in WinList, no events would display. WinList now requests the features from HAPS based on the feature ID instead of feature name.
Removed the "do you want to connect" prompt on app startup. If there's a server name saved in iCyt preferences, WL will attempt to make the connection.
Output resolutions up to 16777216 can now be selected from the Connection Manager.
Corrected a crash that could occur when Log Bias was enabled.
Under some circumstances, region line segments would draw incorrectly when the region's label was moved.
Code has been added to allow the user interface to update during lengthy operations.
Several commands in submenus of the Window menu did not execute the correct command.
When duplicating a data source, the state of the gate list "automatically adjust gates" checkbox is now preserved.
If a report object had no width or height, the PDF creation routine would crash.
Double-clicking a quadstat/nstat label did not perform the "Double-click action" that was set in region preferences. This has been corrected.
Enhanced region creation logic to ensure that region labels are on-scale after new regions are created.
Inactive gates were being recomputed when they did not need to be.
Color by Parameter Value did not assign the last color to as many events as it should have.
When exporting an FCS file using Save Data Source, the parameter resolutions were incorrect if the source file had log-encoded parameters.
When a new file is opened into an existing setup, histogram zoom will reset for any parameters that have a different resolution in the new file compared with the previous file.
When a connection file is not currently loaded and a protocol bundle is saved, WL now stores information about the last connection file in the protocol. It also saves the last connection file in the bundle. This allows the program to enable the "Open Last Connection File" command when the protocol bundle is stored.
Zoom is now reset if a new parameter is selected for a histogram and it has different transformation characteristics than the previous selection.
The auto-adjust routine for HyperLog did not properly handle data where there were no events in the negative portion of the data space. This has been corrected.
The Keywords button on the Open FCS Files dialog did work correctly in some cases.
A misinterpretation of a Millipore InCyte FCS file's $SPILLOVER compensation information has been corrected.
Info windows how update correctly when added to reports.
Macro playback of assigning a gate to a histogram did not work correctly.
The Keywords button on the Open FCS dialog did not work properly.
If a macro-based protocol from an earlier version was opened and modified, WinList could overwrite the macro with a new xml-format protocol when quitting. Logic has been revised so that WinList does not attempt to save changes to a macro-based protocol.
When WL was on a second monitor, the Edit Batch dialog did not position the File dialog next to it correctly.
WL could hang if it moved auto-position regions to the edge of a histogram. On the edge, the logic always considered the region to have moved and tried to process it again.
Result window ID fields can now display keywords from the full results tree.
Network-based, shared "seats" allow multiple users to share WinList as needed, up to the available number of seats.
OpenGL 3D graphics for unique spatial views of correlated 3-parameter data with a host of eye-catching display settings.
User defined keywords and equations create additional analysis results based on keywords and other stats.
Histograms now support data zooming to focus on an area of interest.
Selectable transforms per parameter: HyperLog, Log, and Linear.
Automatic adjustment of HyperLog display settings.
XML-based protocols offer rapid analysis setups.
Create tube-specific compensation using the Compensation Database.
Data Enrich feature allows you to do a “virtual sort” to enhance a population of interest.
Downloadable WinList "Reader" provides an easy and free tool for sharing WinList Reports and analysis protocols.
"Conditional update" areas on reports only update when user-defined conditions are met.
Run a macro script within batch file processing for highly customized batch analysis options.
Report system now includes “smart” positioning of elements as they are added to the report.
Duplicate Datasource now replicates all regions and gates, and colors, keeping the same region IDs.
Gate Statistics window provides stats for all gates, as well as "Unclassified" and "Overclassified" events at each level of the gate hierarchy.
Read and write FCS files in FCS 3.1 format.
Create NStats that label the full phenotype of the FCOM vs FCOM.
The Open FCS file dialog now includes a "Preview" checkbox to preview a set of FCS keywords, making it easy to identify files of interest.
"Show Histograms based on Trace Line Option" arranges histograms based on the selection in the Trace line options listbox to simplify compensation setup.
WinList's main toolbar now contains a drop-down list of coloring modes. Color by Histogram Gate uses the color of the gate that is applied to the histogram. Color by Gate Combinations: this is the new name for Color Event mode. Color by Parameter Value colors events based on the intensity of a selected parameter. Color by Gate Hierarchy uses the color of the last gate in the gate hierarchy that an event belongs to.
Reports now have a "master page" containing items you want on all pages of the report.
Keyboard shortcuts are now provided for adding objects to the report.
A menu command has been added to Check for Updates online.
Gate statistics are now available as keywords in reports and for databasing.
The Edit Gate dialog now allows the user to choose how gates are activated, on a gate-by-gate basis.
The Region preference for NStat sub region labels now includes the option to display name and percent of gate.
The Options menu has a new entry for the Database Update Wizard. This wizard is designed to fix-up region results in existing databases to work with the new structure of WinList. The wizard will check databases, and walk you through an update process for each one.
The macro commands for Save Protocol and Save Protocol Bundle can be edited to replace the file name portion with a keyword. This allows these macro commands to create file names that relate to the FCS file being analyzed.
The macro system can now record and play back the Open Protocol, Save Protocol, and Save Protocol Bundle commands.
1P histogram graphics have several new graphic options and preferences. Choices allow you to overlay color subsets, stack color subsets, or not display subsets.
The Edit Cluster Colors dialog has been replaced by a new dialog, Customize Gate Combination Colors. The dialog is simpler in design, allowing all color combinations to be viewed and edited without having to drill down into a tree.
The Data Sources menu (Window menu) has two new commands to make it easy to activate data source windows. "Next Window" and "Previous Window" activate the next or previous data source windows, respectively.
The Save Data Source dialog has been redesigned to support revisions in FCS standards.
Report windows now have a tabbed control at the bottom which allows page selection and creation.
An option has been added to the Edit Gates dialog that controls whether "cascade gate" mode is on or off.
Reports now support region creation and modification directly.
Significant improvments have been made to 2P graphics.
Each data source now maintains its own regions and gates, rather than drawing from a common set of regions and gates.
Enhanced support for reading very large data files.
WinList interacts with ModFit LT 3.2.1 via DDE for integrated DNA analysis.
User preferences are now stored in protocol bundle files. This makes the bundle file a more complete snapshot of the analysis protocol.
WinList is now compatible with WindowsTM Vista and Windows 7.
The palette and color management system has been redesigned to handle more colors.
The Batch system has been revised to provide a more control over what actions are performed and when they take place. In "Basic" mode, simple options are selected via checkboxes and dropdown lists in the Edit Batch Options dialog. When you need more control, you can put the system into "Custom Scripts" mode. Batch processing levels allow custom actions to be assigned to specific files for detailed control of batch file output.
Histograms can now be “cloned” to create copies with the same graphics and parameters.
A new printing preference has been added to control the size of the output for Print Histogram.
Printing of dots has been improved on high-resolution printer.
A "Palette mode" preference has been added to Histogram preferences to support the new inverse palette option.
WinList now activates any gate that contains at least one valid region. Prior versions required that all regions referenced in the gate expression exist in order for the gate to be valid.
The program now allows the user to locate missing files when opening protocols.
Preferences have been added to set the default transform and its properties.
A WLX protocol file can now be dragged and dropped onto WinList to open the protocol.
WinList now stores the locations of its toolbars, and restores those locations when it starts up.
2P regions now support finer resolution for drawing and statistics.
The Link Regions dialog has been redesigned. It provides support for bi-directional links, and simplifies selection by only showing "compatible regions" that can be linked.
WinList now uses the PnDISPLAY keyword to set default transforms for new parameters.
The cascade gating system has been enhanced so that it can update the chain of dependent cascade gates when an upstream gate is modified.
The Scale-to-Fit data source command now pays attention to the "Keep histograms square" graphics preference.
The quality of the PDF output for reports has been improved.
A new preference has been added to the Reporting preferences to control the "Printed quality" of histogram report graphics.
Gallios and Navios cytometer data files are now supported.
iCyt: WinList can now acquire very large data files, i.e., 20 features and 28-million events.
iCyt: The transformation settings in the Reflection Connection Manager now come from the Transformation preferences. Transformation changes made in the Connection Manager will automatically update preferences.
iCyt: The Connection Wizard now allows easier selection of features. Checkboxes have been added to the feature list to simplify multiple-selection without having to use the Ctrl or Shift keys.
iCyt: WinList now asks the user at start-up whether or not to connect to an iROC server.
iCyt: The Restart button on the iCyt toolbar now works for Monitor mode as well as acquisition mode. When clicked in Monitor mode, all histograms clear and rebuild with new data.
iCyt: The Feature Selection page of the Connection Wizard has been enhanced to provide a dynamic list of feature groups for filtering the feature selection list.
iCyt: 1p histograms now remove stale events if voltage is adjusted on the instrument while WL was monitoring.
iCyt: Sorting regions now work correctly if they are defined in 4-decade mode in WinList. Even with the correction, it is easier to make comparisons between WinList and HAPS Control if WinList is using "computed decades" mode.
iCyt: Text of some iCyt menus and dialogs has been modified so that it makes sense for both Reflection and Synergy instruments.
iCyt: The Restart button on the iCyt toolbar now works for Monitor mode as well as acquisition mode.
iCyt: Acquired files are now stored in floating-point FCS file format.
iCyt: Removed the popup status message that was displayed when data was not received within a timely period.
iCyt: Improved graphics when monitoring. The real-time dots shown while monitoring now correctly accumulate to the desired number of dots before dots are removed. Previous logic removed a certain fraction of dots and rarely displayed the desired number of dots. The new logic eliminates the need for the "Dot Persistence" preference, and provides more saturation in the dot displays.
iCyt: The behavior of color-density, contour plots, and 1P histogram has also been improved when monitoring. These plots will now accumulate events until the desired dot count is reached, and then reset and start accumulating again. For 1P plots, the reset occurs when a peak reaches 1000 events.
iCyt: Behavior change of Dots during acquisition. In previous versions, 2p dot plots would display up to a defined number of dots during acquisition, controlled by the "Max Acquisition Dots" property in iCyt preferences. Once that threshold was reached, no additional dots were displayed. Starting in this version, when that threshold is reached, the histograms showing dots will reset their dots and start accumulating them again. This change allows the operator to see changes in the display throughout the acquisition process.
iCyt: Behavior change when HAPS is pinched or connection is lost . The program now provides more consistent and obvious feedback when it is not receiving data. After 3 seconds of receiving 0-event buffers or no buffers, a small status window is displayed indicating that no data is being received. When monitoring, 1p and 2p plots will reset to show empty plots.
iCyt: Logic has been improved (in some cases corrected) when the user start WinList acquisition mode with the HAPS Control in a "pinched" state. Previously, histograms and results might not reset properly in this circumstance. Now, all histograms and results are cleared and WinList enters a "waiting to acquire" state.
iCyt: WinList now provides support for storing instrument settings in its protocol files.
iCyt Bug fix: Spurious events in an acquired FCS file that had a 0 intensity when the file was reloaded after acquisition have been eliminated.
iCyt Bug fix: When the Finish Acquisition dialog was displayed and left on the screen, memory was being consumed by the acquisition system. Corrected.
iCyt Bug fix: Changing 2p graphics options while monitoring in iCyt mode could cause the program to crash. Corrected.
iCyt Bug fix: Corrected display of dots for low res parameters (event status, droplet status).
iCyt Bug fix: After opening protocol bundles, it was possible that the Edit Connection File command would show incorrect selections. This has been corrected.
iCyt Bug fix: If the Save Protocol Bundle option was set and an acquisition was started and then cancelled, acquisition data was deleted in some circumstances and an empty acquisition file was stored in the bundle. Corrected.
Numerous other bugs were corrected related to the iCyt acquisition plug-in.