Appendix B
History of Delta2D

New Features of Delta2D 3.3

Spot Quality Column

A new column in the quantitation table shows a spot's "quality", i.e. how much the 3D shape of a spot resembles the bell-shape of an ideal spot.

Use Spot Models for Quantitation

Modeled spot shapes will be used for quantitation when they are present.

Spot Detection Parameters Simplified

We have increased the flexibility in spot detection and at the same time made it more robust. Correspondingly, there is a new set of options for the spot detection and quantitation.

Automatic Labeling of Spots in the Quantitation Table

Now you can label selected spots in a quantitation table, using Spot-IDs, or consecutive numbers.

Copy Data from the Quantitation Table to Other Software

Now you can select a range of cells in the quantitation table, press Ctrl-C and paste the data into other documents, such as Excel spreadsheets.

Spot Picking Support extended

Here is a current list of supported spot pickers:

• Genomic Solutions ProPic
• PerkinElmer ProXCISION
• Molecular Dynamics
• Ettan Spot Handling Workstation
• Bruker Proteineer (this entry is disabled because the interface needs additional setup)
• Generic pick list format

Support for Protein Identification by Mass Spectrometry

We have added a number of features that make the data flow from gel images to mass spectrometry and back to gel images more efficient.

Spot Matching Performance Improved

Spot matching was made more efficient and re-matching of a project is now triggered much less frequently.

Better Support for Image Grayscale Calibration

Handling and detection of image grayscale calibrations was improved: the calibration manager now offers to re-create calibrations for all images in the pool.

Better Support for DIGE and Other Multiplex Experiments

There is a new entry in the Warping Strategy dialog that can be used to simplify the setup of DIGE and similar multiplex experiments.

New Features of Delta2D 3.2

Spot Editing

Spot editing has been completely restructured and provides now semiautiomatic adding, splitting and joining of spots.

Multiple Gel Import

Delta2D 3.4 now can import gel images not only one by one but complete sets of images.

Spot Color Coding

A new way to visualize similarities and differences between gel images using colors.

Label Color Coding

See distribution and outliners in isoelectric point or molecular weight of identified proteins at a glance.

Enhanced Label Data

Labels now can carry much more data for spots, such as molecular weight, isoelectric point, gene data, and a lot more.

Plugins architecture

A new interface making it possible to adapt plugins to Delta2D, such as scouts.

Scouts

New plugins fetching proteome data from multiple webbased databases like GenoList, AureoList, Genbank, ...

Mouse Wheel support

Mouse wheel support is now integrated at many places.

pI/MW Calibration

See the estimated pI and Mw for any point on a gel image by pointing with your mouse.

New Spot Modeling

The new spot models are now distinct from each other and do not overlap each other any more.

Performance

Performance again has been increased in many processes.

New Features of Delta2D 3.1.3

Improved Multiplex Functionality

In a special version, Delta2D now supports the use of an internal standard. In a multiplex project all spots are normalized to their correspondig spots on the standard. Delta2D already offers a number of typical channel types but you can easily add new ones.

Gel Image Attributes

Gel images can carry additional information about which gel, sample or channel they belong to.

Enhanced Spot Editing

The requantify tool has been remodeled to add and remove spots more easily.

Matching quality control at a glance

Delta2D now indicates the spot matching quality.

Additional Features in Quantitation Table

A t-test was added to the statistics table and spots can be labeled automatically with their ID.

Performance Improvements

The overall performance again has been increased significantly, making it faster to start Delta2D, view and adjust gel images, and compute warpings of images as well as to detect and quantify spots.

New Features of Delta2D 3.1.2

Performance Improvements

The overall performance has been increased significantly, making it faster to start Delta2D, view and adjust gel images, and compute warpings of images as well as detections and quantitations of spots.

Enhanced 3D view

The three-dimensional representation is now able to show complete regions in the surrounding of selected spots.

Enhanced Image Fusion Capabilities

Image fusion has become more flexible and powerful by letting you apply some pre- and postprocessing to images when fusing them. Additionally, the number of fusion algorithms has been increased to four.

FujiImage Format Added

The generic images produced by Fujiscanners are now supported.

Enhanced File Import Dialog

On importing gel image files, some simple preprocessing like invert, flip, or rotate is now possible to be done.

Improved Design of Quantitation Table

The design of the quantitation tables has been cleared up and improved.

New Features of Delta2D 3.1

Image fusion

Allows multiple gel images to be merged into one average image, or into a proteome map showing all spots that are present on any of the gel images. Resulting images look like real gel images. (see section 4.8)

3D spot view

Three-dimensional views of selected spots, showing single or dual channel images. (see section 5.2)

Expression profiles

Bar charts visualize protein expression levels across a series of gel images. (see section 8.5)

User-defined spot markers

Lets users edit the results of spot detection with minimal manual intervention. (see section 6.5)

Improved spot detection

Higher accuracy, wider spot outlines.

Grayscale calibration

Arbitrary grayscale calibrations can be defined in XML files. (see section 12)

Histogram based filtering

Histograms can be used to visualize the effect of data filtering. Filters can be defined using criteria such as "hide the weakest 10% of all spots" or "hide weaker spots such that the sum of their quantities is 10% of total quantity". (see section 8.2)

User specific settings

User settings are stored in a separate folder for each user.

New Features of Delta2D 3.0

Analyzing sets of gel images

Gel images can be organized into projects, containing groups with one or more gel images. Analysis can be done for gel image pairs or groups. Gel images and analysis results are managed in a central pool.

Multiple quantitation tables

The quantitation table has views for single gel images, gel image pairs, and an aggregated view for gel image groups that shows spot statistics.

Automatic warping

Gel images can be warped automatically. User defined match vectors may be used to guide the automatic warping process.

Improved quantitation tables

Additional columns, e.g. for displaying the symmetric ratio of the master and sample spot volumes.

Improved spot handling

Spots can be cancelled to remove them from the analysis. A set of spots can be selected to be used as a basis for normalization of quantities.

Instant reports in MS Excel

Data from the quantitation table can be used to generate a report in MS Excel.

Instant export to MS PowerPoint

The contents of the dual view can be exported to a PowerPointslide.

New Features of Delta2D 2.1

1. Labels
   • Labels can be placed freely on an image.
   • Full synchronization between labels and spots.
   • Multiple labels per spot.
   • Convenient management of master gel images containing spot identifications.
   • Configurable label formats for master and sample gel.
   • Labels and formats are stored in XML files.
2. Quantitation
   • Spot detection and quantitation can be initiated separately for each gel.
   • Spot boundaries, quantitation data, and quantitation parameters stored in one XML file per gel.
   • Improved data export to spreadsheet compatible files.
3. Quantitation Table
   • Quantitative data can be shown for single gel images or by correspondence.
   • Hide and rearrange data columns.
   • Labels are displayed alongside spots.
   • Spots can be labeled using the table.
4. Spot Picking
   • Centers of detected spots as well as arbitrary labeled points on a gel may be selected for picking.
   • Support for Genomic Solutions and Molecular Dynamics spot pickers.
   • Generic spot picking format.
5. Usability Enhancements
   • New tabs for switching between gel image views.
   • Easier control of background display and histograms.
   • Rollups, e.g. for navigating the gel image.
   • Loading match maps and images in one step.

New Features of Delta2D 2.0

1. Gel Image View
   • Ratio mode to visualize expression ratios directly on the image.
   • User-definable color schemes for ratio mode.
   • Multi-layer display for controlling the visibility of master and sample gel images, background images, match vectors, and spot boundaries
   • Image amplitude rescale
   • Adjustable automatic prescaling of large images
2. Background Subtraction
   • Background can be excluded from visual and quantitative analysis.
   • Background levels are computed based on image regions.
3. Spot Detection
   • Advanced image processing algorithms.
   • Small set of user-defined parameters.
   • Spot boundaries are overlayed on the dual view.
   • Full synchronization between dual view and quantitation table.
4. Quantitation
   • Automatic background subtraction.
   • Computation of spot centers.
5. Quantitation Table
   • Display spot correspondences.
   • Sort according to any numerical column.
   • Filtering rows.
   • Mark and hide spots / rows.
   • Automatic counting of total/visible/selected rows and spots.
6. Spot Matching
   • Fully automatic spot matching according to match map.
   • Robust matching algorithm, no need for manual corrections.
7. Data Export
   • Data can be exported to CSV format for easy processing. using spreadsheet software (e.g. MS Excel) and other analysis packages.
   • Export of spot centers.
   • Rows can be selected for export based on quantitation table's sorting and filtering.