ModFit LT™

Productivity

Fast, accurate, automatic analysis

Trained on thousands of sample files, ModFit LT features a robust automatic analysis engine. With sophisticated peak detection, the system identifies ploidy patterns and dynamically creates models to match. Improvements like AutoDebris™, AutoAggregate™, and AutoLinearity™ make analysis more robust and consistent from one user to the next.

Cycle Analyzer™

Ploidy determinations are no longer bound to the peak order. Make use of internal standards or an external reference to determine which cycle is classified as Diploid. Any number of cell cycles can be analyzed.

Customized reports

From letterhead graphics to text, ModFit LT imports from the clipboard everything you need to create your own reusable report templates. Save your custom reports with all the text formatting, analysis information, and even the histogram data.

Stored comments and impressions

Create your comments just once and ModFit LT allows you to store them in a quick retrieval database. You provide a convenient description for the comment and ModFit LT does the rest.

Database and graphic output

ModFit LT allows you to automatically add to a database each time you analyze a data file. Select the items you want to database from an extensive list of results and keywords supported in the sample. Output is in a simple tab delimited format so it can be easily opened by programs like Microsoft Excel and laboratory information systems. Histograms and report graphics can be easily exported in standard graphic formats for use by other programs.

Batch processing

Process groups of data files with ease using ModFit LT. The batch system automatically loads data, analyzes, and saves reports and graphics. Plus, you can batch process reports for easy review of analysis and printing. Convenient VCR-style buttons make it easy to move through the batch of files or reports.

Flexibility

Automatic and manual analysis

While auto analysis is used for the majority of histograms, you can take control of scaling, model selection, and range positioning for manual analysis. A Quick Model Editor makes it easy to make adjustments to the model.

Configuration options

Your system can be custom configured for linearity, S-phase modeling, number of standards, and model colors used by the program. In addition, peak finding adjustments can fine-tune the program to the subtleties of your data. With three levels of security, all important configuration options are password protected.

Listmode gating

Create up to two, high-resolution, 2-parameter gates to select the data to be analyzed. Three predefined shapes make gating quick and efficient, yet each can be modified with the click of a mouse. Gate graphics appear on the report page automatically, making live gate adjustments a snap.

Customized histogram graphics

Just double click on the histogram and you have complete control over axis tic settings and display options. Editing axis labels and fonts is quick and easy. And zoom graphic objects allow you to see many views of the histogram at the same time.

Keywords

Any keyword from your data sample can be databased or included in your reports. In addition, all analysis results computed by ModFit LT can be accessed for databasing and reporting.

DDE support

Windows versions support Dynamic Data Exchange (DDE), allowing users to create custom extensions and automation solutions.

Accuracy

Proven Models

Models built from Gaussian, rectangle, trapezoid, polynomial, AutoDebris™, and AutoAggregate™ components are processed by a Marquardt nonlinear least-squares analysis. The models used in ModFit LT have been tested with thousands of histograms to ensure accurate results. Analyze samples with any number of cell cycles and multiple internal standards.

Quantitative S-phase assessment system

Based on a statistical method for determining the standard deviation for the S-phase estimate, ModFit LT provides a p-value for classifying your S-phase result within your laboratory cutoffs.

S-phase cutoff values

Enter your S-phase cutoff values for any type of tissue you analyze. Separate cutoffs are provided for DNA Diploid, DNA Aneuploid, and Total (Average) S-phase percentages.

Synchronization and Proliferation wizards

Analyze synchronized cell lines and other perturbed samples with powerful models created by a simple-yet-sophisticated wizard. Choose from options in the wizard dialog to match the model to your data, and let the wizard do the rest. You can even analyze cell-tracking dye samples with the new Proliferation wizard.

Ease of Use

Simple function toolbar

Each analysis option is represented on a toolbar with a symbolic button. Conveniently arranged by function, the buttons speed your typical analysis, whether using automatic or manual mode.

Context sensitive on-line help

For a quick reminder or to look up a function, help is available on-line. ModFit LT's help system provides searching and browsing through virtually all of its documentation.

Short learning curve

Simple design and operation has enabled us to create a program that is easy to learn and use. The interface offers surprising consistency from one platform to the next. We have even created video tutorials to help you get going as quickly as possible.

Available in versions for Windows 2000 and later, as well as Mac OSX 10.3 and greater.

New Features

These are the latest features added to ModFit LT:

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)

Testimonials

Starting as a student in the lab of Dr. Cees Cornelisse in Leiden, The Netherlands, I worked with an ICP22 and had to calculate the DNA index and S-phase manually from histograms plotted on calibrated paper. The introduction of the FACScan allowed us to experiment with multiparameter DNA analysis. The combined use of WinList and ModFit was a blessing from the sky. Currently, we perform multiparameter DNA flow cytometry on a daily base using ModFit and WinList for analysis. Especially the collaboration with "The Guys from Verity" is inspiring and results in a continuum of sophisticated improvements of WinList and ModFit.

Willem E. Corver, PhD Dept. of Pathology Leiden University Medical Center The Netherlands

"I've been using ModFit since version 5.1 (1992). I've still got the manual from that version, and the cover says "DNA Analysis Advances into the Next Generation". It did, and still does - with LT. Incredibly full-featured (more than I know what to do with). The accompanying "Rule-Based Analysis System" is probably the best software documentation I've ever seen – not only for how an application works, but how to USE it."

Marc Langweiler, DVM, PhD of Dartmouth-Hitchcock Medical Center

"I have been using ModFit LT since its inception and find it to be the most robust and simultaneously easy-to-use software tool for DNA-ploidy /proliferation analyses on the market. Every time I fire up the program, a wee dram of my favorite single malt drips from my mouse pad."

Frederic I. Preffer, Ph.D. of Massachusetts General Hospital

"Standardized DNA flow cytometry adds valuable information to the diagnosis and prognosis/prediction of different malignant diseases. Thanks to accepted guidelines, high performance instrumentation and finally, but none the least, evaluation software like ModFit LT, it is possible to get safe and reproducible data. Especially, this is the fact when ModFit LT is turned into automatic mode. ModFit LT is used by all DNA flow cytometry laboratories engaged to the Swedish Society of Flow Cytometry (http://www.sfff.se/). Just click on the Auto fit button and ModFit LT will do a perfect fit!"

Bo Baldetorp, Professor, of Department of Oncology, Lund University

"I've been using ModFit LT for cell cycle analysis since the early 90's, and it's never let me down. The software is easy to use, and is very capable of handling the most demanding samples as seen in a multi-user core cytometry resource. I especially value the personal attention and cooperation of the technical staff."

Peter Lopez, Res. Assistant Professor of Pathology of NYU Medical Center

"We have been long time ModFit LT users, both in a research setting and with clinical samples. The cell cycle models give us the answers we need to examine proliferation of T cells or the effects of drug treatment in tumor cell models. We find the proliferation wizard particularly useful, analyzing cell generations stained with CFSE. As always, the best part of ModFit is the support we have received over the years from guys at Verity."

Richard Cross, Ph.D of St. Jude Children's Research Hospital

"ModFit LT is a critical component in our Core Facility for quantitative DNA cell cycle analysis and cell proliferation assays. It is easy to use, robust, reproducible and has superb technical support."

Richard F. Konz, Jr. of UMass Medical School

"As director of a Clinical Flow Cytometry lab and a Flow Cytometry research core, I have used Modfit LT since 1994 and have found it to be an excellent solution for our DNA analysis needs. ModFit LT is versatile and can be used for the analysis of DNA Cell Cycle alone or cell cycle combined with population based surface markers, cytoplasmic markers, nuclear proteins, cyclins, oncoproteins, BrdU, Tunnel, etc. ModFit LT has automatic analysis features as well as models that can be selected manually to fit a variety of diploid and aneuploid situations. And, the ModFit LT Sync Wizard provides great statistically relevant models for the explanation and interpretation of raw research data. Goodness of fit statistics are provided for each model and (so long as the staining has been done competently) I usually strive for a chi square (rcs) less than 4 for research samples. I've used ModFit LT to analyze numerous synchronization studies in pharmaceutical trials to look for perterbations to the normal cell cycle for that particular cell line. Linking ModFit LT to WinList produces a powerful tool with the combined analysis of Cell Cycle and surface, cytoplasmic, nuclear or all four simultaneously. Clinical analysis is automatic and superb. Research capabilities are varied to fit the many cell cycle possibilities that come our way from the huge variety of cell types and species in most research settings. I highly recommend ModFit LT as an analytical tool for those who wish to get the most out of their DNA data."

Jim Price, Ph.D. of Vanderbilt University & VA TVHS Nashville

"ModFit and WinList are two great flow cytometric programs, backed by a company with a strong commitment to customer service and satisfaction."

Paul K. Wallace, PhD, Director of Flow Cytometry of Roswell Park Cancer Institute

"In our Core Laboratory, ModFit LT has worked out perfectly for us. With investigators studying varied model systems and instrument users of all different skill levels with respect to flow cytometry and data analysis, finding software that everyone can use is often difficult. ModFit LT allows us to define the level of software access for each user, from novice to advanced; in that way they can safely perform cell cycle analyses only within the scope of their training and understanding of software modeling. This flexibility, coupled with the help of training using the ModFit LT Rules Based Analysis System, has allowed many of our investigators to learn the software rapidly and correctly analyze their data. The best part is that the training resource is so easy to follow that much of it can be learned independently, which reduces the time demands on our two-man staff!

Wayne Green of Flow Cytometry Core Lab, University of Utah Health Sciences Center

"I have used ModFit LT software to model our DNA ploidy samples since the first versions in 1994. I love the flexibility in all (Verity Software House) software products which allows me to "tweak" the analysis to my personal preferences. This is a luxury we don't see in other Flow Cytometry software applications. I have found the ModFit software very easy to use since we can model a case in about 10 seconds using the Automatic Analysis button. The results are accurate and the layout is easy to comprehend. On difficult cases, we can choose the manual mode and print multiple analyses of the same listmode file for the pathologist to decipher. I would recommend this product (and have) to anyone performing DNA ploidy analysis by flow cytometry.

Avis Peters MT(ASCP) QCYM of United Hospital