ModFit LT New Features

These are the latest features added to ModFit LT:

Version 5.0 (January, 2017)

New Features:

Gating is no longer restricted to 3. Up to eight gates will fit nicely on the report.

Added a graph showing the “residuals”, data not accounted for by the model.

Added log-like transforms: HyperLog, Hyperbolic Sine, and VLog.

Negative values can now be displayed in the histogram graphs.

Added compliance mode and enhanced logging.

Custom model equations can now be added to the database and report.

Added SVG graphic output.

Added a database wizard to add common results to a database automatically.

The user interface has been redesigned with a ribbon bar with new, more informative icons and labeling.

Improvements:

User equations can now be applied to a specific model type.

Equations shown on the report can now be edited.

Drag and Drop has been added for many items.

Added more results for cell tracking analyses.

Added editing of multiply selected objects.

Improved editing of graphical and text objects.

Prevented multiple users from accessing a database file at the same time.

Gates referring to measurements not in the current file will now be shown on the report indicating that the measurements are invalid.

Improved FCS file loading speed.

Improved the handling of the expected diploid position for samples where the position of the standard was higher than the expected diploid

Changed the component color transparent property to percent transparent.

The page size and margins can now be edited by right clicking on the report page.

Printing will more exactly match what is shown on the screen.

Keywords shown on the report can now be edited and displayed in free-form manner.

Improved the speed of printing and PDF creation the first time after ModFit is run.

Added an option to the Options and Configuration to adjust the quality of PDF output. This allows for the creation of PDF files that are smaller in size.

Added an option to prevent overwriting of reports and other output during batch processing.

Improved the 2P density plots in the case that a large number of events was "piled up" at any of the edges of the displayed range.

Bug Fixes:

The histogram resolution (channels) saved with a report will now be used when analyzing additional data.

Prevented opening a database key file as a database.

File New now completely resets the properties of the report objects.

Fixed a bug that caused an unexpected "transform has changed" message when loading the same FCS file into a report

Fixed a bug that caused incomplete drawing of cell tracking components if the graph scale was changed.

Fixed a bug that caused the x-zoom graph to show the full scale after reading a report.

Fixed a bug that prevented the database backup feature from working.

Deleting a model range will no longer cause unexpected modeling results. Affected components will either be disabled or adjusted

The MF_GATEn_PERCENT results now reflect the percent of events that pass the nth gate.

Fixed a bug that caused region movement to be a little jerky.

Fixed a bug that caused the Aneuploid Fraction shown in the Fit Diagnostic objects to be incorrect for Tetraploid models.

Fixed a bug that caused the SD value used in the cell tracking wizard to change when "Lock SD" was checked.

Fixed a bug that could cause the parent position cursor to be at channel zero in the cell tracking wizard after loading a report

The logo text was clipped in a PDF output if the report was zoomed to 50%.

Fixed a potential crash if the OK or cancel button was double clicked in an editor.

Fixed a bug that would cause incorrect spacing of generations if parameter zoom was applied.

Fixed a bug that could cause a crash if ModFit failed to save the auto-recover files.

Fixed a bug that caused a crash after showing region vertices, creating a new region, and then trying to move it.

Fixed bug that caused the report graphic export created via the batch processor to always go to the "ModFit LT for (platform)" path in the user's document path.

Fixed a problem that caused the cell tracking analysis to fail if some generations have a mean of zero or less.

Fixed a crash that could occur while in the trial period if the settings were reset.

Fixed a bug that could lead to a crash in some cases if a file was opened and then became unavailable.

Fixed a problem that prevented the Check for Updates command to find updates.

Changes to the file and report batch settings will now be remembered.

Version 4.1 (August, 2014)

Note: The Mac version runs on Intel Macs. PowerPC Macs are no longer supported.

New Features:

Added [AutoLinearity()] DDE command handling.

Added equations and results for models generated by the Cell Tracking Wizard.

Added equations and results for the shape of the S-Phase components.

Added equations and results for the state of the G1 position in the sync  wizard.

Equations added to custom models are now added to keyword results, allowing the values to be added to the database.

When building custom models, it is now possible to have ranges "auto-position" to a specific peak in the histogram.

Added a Copy to clipboard to the database.

Simple analysis estimates will now update as ranges are moved and will display the mean and SD in the status bar or tool tip when moving a range.

The X-zoom graph can now be set to adjust to the Dip-G1 or the cell tracking parent peak position using a new option in the Options and Configuration.

Automatic backup and recovery: We've designed a new automatic backup/recovery system. The system will save a copy of your report into "My Documents/ModFit LT for Win/AutoRecover" every 2-minutes by default. A property, "Save Recovery Backup", has been added to the Options and Configuration to specify how often the backup is created. In the event of a crash, power failure, or other abnormal termination, ModFit LT will check the AutoRecover folder on next start-up and allow the user to recover any auto saved reports.

Automatic crash detection and reporting (WINDOWS ONLY): We've added a new crash reporting system that creates a ZIP file with information that Verity can use to pinpoint the crash location in the software. The Crash Reporter will offer to send a crash report to Verity, as well as to restart ModFit LT after a crash. Users can choose whether to include the application log (if active) and any auto-saved ModFit LT reports with the crash report. Crash reports are saved into "My Documents/ModFit LT for Windows/CrashReports"

Added keyboard shortcuts for "Auto Analyze and Auto Linearity" and "Fit with currentmodel".

Added "Auto Analyze and Auto Linearity" to the Analysis menu.

Added options to customize the appearance of many of the report objects.

Improvements:

Added new logic that will detect when zooming is needed and apply zooming to measurements in Accuri data files. The user is notified and given a chance to adjust the zoom via a timed notification message.

Using a more accurate method for determining the zoom to percentile boundaries.

Made changes to when information about parameter names, transforms, zooming, etc. are stored in the parameter database. An entry will only be stored if an edit is made and the user answers yes to the question: "Do you want ModFit to remember these settings for [Parameter Name]?". This change should prevent confusion regarding parameter display properties and defaults.

Changes made to the graphs in the Analysis Setup dialog will now be reflected in the report graphs, and the reverse.

The user login has been disabled by default, go to Edit Options and Configuration to re-enable it if needed.

One can now correctly specify and use Gaussian components with multiple compartments.

One can now create a new model component from scratch rather than simply duplicating an existing component.

The model's fit line preferences can now be edited via Edit Colors.

When a standard is added or edited so that its expected position is less than the peak finder's Start At setting, the user will now be asked if that setting should be adjusted automatically to allow a peak to be found at the expected position of the standard.

Clarified and added options that are shown when a sample analyzed by the synch wizard with a floating G1 position and a peak is not found in the expected range.

The lower limit for AutoLinearity has been lowered so that it can be set to values as low as 1.80.

The debris component, aggregate component, and RCS calculation will now ignore events in channel zero. This prevents issues when a large pile up of events is present. This change will cause ModFit LT to get different results for the same analysis as previous versions. However in most cases it will have little if any effect.

It is now possible to move an equation up or down in the equations editor.

Simplified the file and report batch options by removing the Auto Linearity checkbox. The auto linearity option is now add as part of the analysis mode.

Added options to the full model editor to edit the fit line style and weight.

Added copy and paste context menu entry for objects on the report page.

The Y-zoom graph will now adjust its x scale to match the main analysis graph.

Bug Fixes:

Fixed a bug with the calculation of generation SDs and thus the Division Error Index when using the proliferation wizard and ADC channels. This bug caused the SDs of the generations to be incorrectly computed on linear values rather than log channels.

Proliferation analysis of DDE data will now use the correct number of decades to compute the generation spacing.

Fixed a bug that prevented editing of parameters after reading a report that contained an analysis of listmode data before opening a listmode data file or after opening another file type (histogram, ASCII, DDE). This bug also caused the axes to be labeled "Channels" instead of with the listmode parameter names.

Fixed a bug that causes the incorrect transform to be applied. A linear encoded FCS parameter will indicate that it is being displayed as log and vice versa. If the user attempts to analyze a linear FCS parameter in this case, LT would think it is a log parameter and the analysis will fail. If the user tries to manually change to the correct transform the data will be incorrectly transformed, for example linearizing a linear encoded FCS parameter. The problem occurs when a parameter is loaded with one encoding (linear vs. log), and then subsequently a parameter with the same $PnN and $PnS is loaded that is encoded in the opposite manner.

Fixed a bug that occasionally caused the drawing of a visual artifact in the debris area of the fitted histogram.

Fixed a bug that would cause a crash in Auto Scale-Y was turned off and a gate graph was selected in the analysis setup dialog.

Fixed a bug that would prevent choosing a database with the same file name in a different directory.

Fixed a bug that would cause a crash if the Cell Tracking Wizard was run on an ASCII file, histogram file, or DDE data.

Fixed a bug that caused the parameter zoom to be incorrect when the parameter was encoded as log in the FCS file and displayed as linear in ModFit LT.

Fixed a bug that caused a database entry to be added for both the initial analysis (auto or fit with current) and the final analysis when auto linearity was checked in the file and report batch properties.

Fixed a bug that caused regions to obscure the data in PDFs generated from the report. This also fixed errors that would be found on the generated PDFs when loaded into certain PDF readers.

Fixed a bug that prevented the opening of listmode FCS data after doing a DDE connection from WinList.

Fixed a bug that caused a crash if a 1024 res histogram was loaded and then DDE data was pushed over from WinList.

Version 4.0 (March, 2013)

Major improvements:

New Analysis Setup dialog for listmode files
The gating and analysis parameter selection dialogs have been redesigned into one streamlined dialog that provides access to all gates and gating tools with improved ease and better graphics.

New region tools
Gating regions can now be created with a full compliment of region types, including freehand regions.

Improved 2P graphics
We have overhauled the graphics for the 2P gating plots to provide better visualization and publication quality.

Parameter selection
For listmode files, the parameters displayed on 1P and 2P plots can now be changed by clicking on the axis label and selecting a new parameter from the list.

External keywords in XML files
ModFit can now read XML files containing additional keyword information and display those keywords on reports and in the database.

Display log or linear axes
ModFit now supports both log and linear axes and presents results in the units displayed on the axis.

Log axis based on FCS file keywords
The program now makes use of keywords in FCS files to determine whether an axis should be display in log or linear.

Parameter zoom
When reading listmode files, ModFit can automatically zoom in on a portion of the data based on several user-selectable methods.

Parameter database
User selection of parameter alias, zoom, transform, and scale are stored in a parameter database.

PDF support
ModFit can now generate PDFs of the report, including during batch processing.

Compensation from keywords
When ModFit detects compensation information stored in FCS file keywords, it can now read and apply that compensation automatically.

Auto-linearity access improved
Auto-linearity is now available via a tool button, file batch processing, and while using synch wizard. There is also a keyword that indicates whether auto-linearity has been performed.

Choose Dataset for multi-dataset files
For listmode files containing more than one dataset, such as FC-500, Galios, and Navios files, the program now allows selection of the dataset at any time via a command in the File menu.

Improved graphic output
The program now offers a Copy Special and graphics export preferences to allow output of high quality images to clipboard and disk.

OLE support eliminated
OLE support has been eliminated from the program.

Bug Fixes:

If text in the Keyword object was edited by the user, the edits where not stored and did not appear on the report. This has been corrected.

Fixed a crash that would occur if the graph object was edited before data was loaded. File -> New will now completely clear the report and properly reset to the original state.

Ranges will no longer move to the top left of the graph and be stuck there if no peaks are found.

The DDE example script would fail if an analysis had not been done before it was run.

ModFit will now correctly interpret keyword values sent from WinList via DDE.

Pasted images will now properly allow for transparent areas.

The axes can now correctly display tics for values less than 1.0.

Component colors will now be displayed correctly when Transparent is not checked.

 

Version 3.3 (July, 2011)

Graphics more responsive on the Mac

"Auto-zoom" has been added for proper scaling of data acquired on Accuri systems.

The Synchronization Wizard has been improved.

Connections to WinList have been improved.

A number of fixes and enhancements have been made to the Full Model Editor.

Minor bug fixes have been implemented.

Version 3.2 (July, 2008)

This version supports native OSX on the Mac platform, and Vista on the Windows platform.

We have removed OLE automation support from this build. Please contact Verity Software House tech support if you would like to see this added back in a future release.

Graphics are now bitmap format instead of vector format for clipboard and disk files.

A number of bugs have been fixed.

Version 3.1 Service Pack 3

The program now supports high-resolution, digital data up to 32-bits. This includes support for 18-bit FCS data files exported by BD's Diva software. 

A "Convert" button has been added to the listmode Choose Parameter dialog. This button displays the Edit Properties for Log Conversion dialog that allows linear parameters to be converted into log parameters. Use this option when reading Diva-generated files that were stored in linear, FCS 3.0 format. The dialog displays a list of all parameters in the file, allowing the user to select parameters to convert to log for display and analysis. It also provides an option to convert to 4-decades or the "computed" decades for the native, linear resolution.

The program now supports FCS files containing more than one dataset. When a multi-dataset file is opened, the program displays the Choose Dataset dialog to allow the user to select the dataset which should be used for analysis. The selection remains in effect until it is invalid or the user makes a new choice. The dialog can be redisplayed by enabling the "Multi Dataset Prompt" property in the File Batch Settings dialog.

When the program is configured to base ploidy determination on an external reference or an internal standard, several new results are reported. The results will display a "Reference Diploid" value that shows the location where the Diploid G1 is expected to be. In addition, each cell cycle shows a "DI based on reference:" statistic, which is computed as the G1 mean of the cycle divided by the "Reference Diploid" value. For all cycles except Diploid, the typical "DI" is also still reported.

A new function has been added to the equation processor. The "F" function can be used to convert a keyword value into a floating-point number. This allows the keyword to be used in calculations. The syntax is: F[expression], where expression is typically a keyword. For example, the $P1B keyword stores the number of bits used to store a value for parameter 1 in an FCS file. 

New internal keywords have been added to provide access to the External Reference Mean [ExtRefMean], and the Diploid-to-Standard Ratio [DipToStdRatio]. 

The SetProperty DDE/OLE command has been enhanced for the ExternalReference property.

A new ploidy index of -1 has been added for hypo-diploid models. Ploidy index can be displayed using the MF_PLOIDYINDEX keyword. 

Bug fix: Program crashed when S-Phase component was changed to a single Gaussian. This has been corrected. 

Bug fix: The Mac version did not properly list files on some network drives. When the network drive was selected, files in the application folder were displayed. Corrected. 

Version 3.1 Service Pack 2

This service pack includes all of the corrections and enhancements of version 3.1. It can be applied to a ModFit LT 3.0 or ModFit LT 3.1 installation.
The Proliferation Wizard now detects conditions where there is little or no Parent generation. The wizard locks the SD for the Parent to the last known good SD and alerts the operator. This addresses problems that could occur in analyzing a sequence of proliferation data files where the Parent generation is not present as the experiment progresses. 
The X-zoom graphic is now placed behind the main graph by default, instead of on top of it. It can be moved to be on top of the main graph by selecting the main graph, choosing the Report->Send to back command, and then selecting and moving the zoom graph.
Implemented "battery" usage system. 
Bug fix: Corrected crash that could occur when an older version of the proliferation model was opened in a report and used for analysis in a newer version of the program. 

Version 3.1 Service Pack 1

This service pack includes all of the corrections and enhancements of version 3.1. It can be applied to a ModFit LT 3.0 or ModFit LT 3.1 installation.
The program now supports 3 gates and displays gated data in the second and third gates. See the Listmode appendix for more details.
Prolif wizard now supports export of "partition" information. Options for export appear on the Other tab of the prolif wizard dialog. A new tutorial describes how this feature can be used with WinList to provide enhanced proliferation analysis.
The Proliferation wizard now supports a "floating" model option for the daughter generations. On the Generations tab, you can choose between the "Standard" and "Floating" model options. In the standard model, the mean of each generation is dependent on the previous generation, based on the spacing value. In the floating model, a range is associated with each generation and the mean is allowed to 'float' in the model. This option should ONLY be used with well-defined, visibly-separated generations.
Added a Lock SD option to the Parent Tab of the Proliferation Wizard. This option is useful for proliferating samples in which the parent population becomes indistinct. When the option is enabled, the SD for the parent population can be edited. All generations use the same SD as the parent, regardless of the state of the Lock SD option.
The status bar now displays low and high X and Y values as gate regions move or resize to allow for more precise positioning. You can also display the position of a region by clicking and holding on the region without moving it.
When the program opens, it is now positioned and sized to the location and size which were last used.
The registration dialog now displays a confirmation dialog when a valid unlock code is entered.
The User Login name is now stored in a keyword, MF_USERLOGIN, which can be displayed on reports and stored in the database.
The program now uses the Unbiased Summation method for reducing histogram resolution to 256 channels. This will likely improve RCS values for histograms that have native resolution greater than 256-channels. It may also result in slightly different locations for peaks found by the Peak Finder.
After selecting a batch of data files or reports, the program now automatically displays the Edit Properties for Batch dialog to allow batch properties to be adjusted prior to opening the first file.
Options and Configuration now provides separate options for auto-scaling X and Y axes to allow greater control.
Bug fix: User edits to the X axis label are now left in place when new data files are opened. If first characters of the label are the default label "Channels", the program will auto-label the axis. Otherwise, the user label is left alone.
Bug fix: Graphics now update correctly for first-time DDE connection with Winlist on PC.
Bug fix: The program could crash if gating resulted in zero events in the histogram. The crash would occur when trying to fit the histogram. This condition could also occur with DDE connections to WinList.
Bug fix: The Proliferation Wizard did not reposition the parent range if the parent position was adjusted in the dialog when editing the model. This led to cases where the model would fail to fit some files if the parent population moved beyond the scope of the range.
Bug fix: program could crash if low or high channels for zoom graphics were greater than 256 channels AND preference settings for Desired Resolution were 256. Crash would occur when a new data file was read into the report.
Bug fix: program could crash with file or report paths greater than 120 characters. Revisions now support paths to 250 characters.
Bug fix: When batch analyzing files using the "Fit with current model" option, the program would slow down as it progressed through the batch. An internal array was not properly cleared in this scenario.
Bug fix: With auto-scaling disabled, user-defined scale didn't apply when advancing to next batch file while in scale view. This has been corrected.

Version 3.1

Several new keywords have been documented.
The Edit Keywords dialog now uses an Add button instead of a Copy button. The added equation will have a standard default value.
OLE features have been enhanced to provide more extensive OLE Automation capabilities.
A Reset button has been added to the batch controls.
A new AutoAnalysis setting has been added to make all G2M's dependent. By default, this setting is enabled. This is a SIGNIFICANT CHANGE from previous versions that greatly improves operator-to-operator consistency.
The logic that detects shifting of positions of internal standards has been improved.
Crashes that could occur if AutoAnalysis could not create any cell cycles in the model have been corrected.
Options and Configuration now has an Overrides section that can apply settings to models in reports as they are loaded.
Models now have the ability to ignore internal standards in the generation of debris and aggregate components. By default, internal standards are now ignored by these components.
The Full Model Editor now displays the component ID when showing the list of components in the model.
Bug fix: Sync and Prolif wizards didn't clean out analysis keywords from database or keyword objects. Corrected 30Jul2001 (vi 969)
Bug fix: Debris component could report negative percentages and areas in unusual cases. Corrected 30Jul2001. (vi 999)
Bug fix: The program did not read INCLUDE equation files from the model's path if a model was opened in the Full Model Editor. Corrected 26Jul2001.
Bug fix: A crash occurred when a model component (other than the last component) was deleted from a model with the Full Model Editor. Corrected 25Jul2001 (vi 1010)
Bug fix: A crash in peak finder could occur when a histogram had no events. This unusual case could occur in a DDE connection with WinList when the histogram in WinList is gated and shows no events. Corrected 25Apr2001
Bug fix: The program can now identify hypo-diploid conditions where the hypo-diploid peak is at a lower channel than an internal standard.
Bug fix: The program now defeats S-phase cutoff warning when in OLE automation mode. Corrected 4Sep2001 (vi 294)
Bug fix: A custom model in saved report did not "fit" when the report was re-opened. Corrected 4Sep2001 (vi 975)