Syngene >> Dymension

Dymension is revolutionary software that can analyse a typical 2D gel image rapidly. It features novel algorithms for background subtraction, noise filtering, precise warping, spot detection, rapid matching and reduced image editing time. Using its powerful spot detection algorithm, Dymension instantly locates and analyses protein spots. With Dymension, the entire analysis process from background correction to spot matching results and reporting takes minutes, making this the fastest 2D gel analysis package currently available.

Dymension is available in three versions, and upgrading between the packages is simple.

• Dymension 1. Dymension 1 is ideal for users looking for software to analyse spots between samples containing one 2D gel only. It offers a range of automatic image correction features and methods of resolving and analysing spots on single gels. The software can be easily upgraded to Dymension 2 or 3 if the proteomics needs of the laboratory change.
• Dymension 2. Dymension 2 has all the features of Dymension 1 but has the added ability to detect and compare protein spot maps in samples containing replicate gels. The software offers many background correction and noise filtering features including a SYPRO® Ruby filter, which can detect and automatically remove spots caused by SYPRO® Ruby crystals adhering to the gel, thus saving users valuable time editing their image. Dymension 2 is suitable for users that need to determine the amount of protein present before and after drug or protein induction treatments. The software automatically detects and assigns statistical confidence to each and every difference in spot normalised volume, thus accurately highlighting proteins of specific interest. The results of the analysis are displayed as a dynamically linked table, 3D spot profile, bar chart, correlation and scatter plot, which make it easy to compare many expression profiles simultaneously and therefore accurately pick proteins suitable for further analysis.
• Dymension 3. Dymension 3 is exciting software, which has all the functionality of Dymension 2 so can be used to analyse samples containing replicate gels. Dymension 3 has the additional capability to analyse multi-stained fluorescent gel images stained with up to three contrasting labels, eg, Cy™2, Cy™3 and Cy™5. This feature allows users to analyse multiple sets of any type of 2D protein gel, regardless of how it was stained, using only one software package.

Dymension 1 Features

Feature	Benefit
Icon driven user interface	Simple software set-up and use
Accepts data from a TWAIN source	Versatile as accepts gel images generated by most commercial scanners
Experiment set up wizard	Fast, comprehensive analysis
Process flow chart	Easy guide for user from image loading to obtaining results
Automatic background correction and noise filtering	Saves time with spot editing
Automatic and precise sample warping	Faster spot matching
Revolutionary spot detection algorithms	Rapid spot detection and splitting
User definable spot detection parameters	Flexible as allows user adjustments
Spot editing and filtering functions	Control of spot editing and filtering parameters

Dymension 1 Specifications

Component	Description
System	Software for the rapid analysis of 2D protein spots between samples containing one gel only stained with visible or fluorescent dyes
On screen views	Syncronised zoom with intensity autoscale
Image processing	Automatic and precise image warping with vector view, background correction and noise filtering
Spot detection	Automatic spot detection
Speed of spot detection	3x10 Mbyte images in eight seconds
Spot matching	Automatic spot matching
User definable parameters	Spot detection with user adjustable parameters. Spot editing and filtering. Spot normalization
Image calibration	pl and MW ladder calibration. Protein list assignment of spots with known identity, pl and MW
Power input	Data visualisation

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Dymension 2 Features

Feature	Benefit
View results in a dynamically linked table, 3D spot profile, bar chart, scatter and correlation plot	Easy to compare many expression profiles simultaneously and quickly select proteins of interest
Exports coordinates to automated spot pickers	Fast and precise interface between Dymension and spot pickers
Automatic filtering of SYPRO® Ruby crystals	Saves time with spot editing
Optional Gaussian spot fitting	Choice of spot detection models
Automatic and precise replicate warping	Faster spot matching as the replicate images are properly aligned
Automatic matching of samples containing unlimited number of replicates	Improves accuracy by reducing manual editing time
Internet links to federated databases	Quick presentation of protein sequence and structure
Dyversity compatible	Direct analysis of GLP secure images using the Dyversity unique capture system

Dymension 2 Specifications

Component	Description
System	Software for the rapid analysis of 2D protein spots between samples containing replicate gels stained with visible or fluorescent dyes
On screen views	Main pane and secondary panes for viewing replicates and samples. Syncronised zoom with intensity autoscale
Image processing	Automatic and precise image warping with vector view. Manual warp editing. Automatic background subtraction and noise filtering. SYPRO® Ruby Crystal filter
Spot detection	Automatic spot detection. Region of interest option. Gaussian spot modelling option
Speed of spot detection	3x10 Mbyte images in eight seconds
Automatic spot matching	Automatic warping and spot matching across multiple samples
User definable parameters	Spot detection with user adjustable parameters. Spot editing, filtering and normalisation
Image calibration	pl and MW ladder calibration. Protein list assignment of spots with known identity, pl and MW
Data visualisation	Interactive process flow diagram. Histogram (brightness and contrast). Main pane and secondary panes for replicates and samples. Bar chart. 3D spot profile. Table of spot matching results. Scatter plot. Correlation plot.

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Dymension 3 Features

Feature	Benefit
View results in a dynamically linked table, 3D spot profile, bar chart, scatter and correlation plot	Easy to compare many expression profiles simultaneously and quickly select proteins of interest
Exports coordinates to automated spot pickers	Fast and precise interface between Dymension and spot pickers
Automatic filtering of SYPRO(R) Ruby crystals	Saves time with spot editing
Optional Gaussian spot fitting	Choice of spot detection models
Automatic and precise replicate warping	Faster spot matching as the replicate images are properly aligned
Automatic matching of samples containing unlimited number of replicates	Improves accuracy by reducing manual editing time
Analysis of multiplexed and non-multiplexed gels	Cost effective as one software will analyse all types of 2D gel stains (eg Cy2, Cy3, Cy5), SYPRO® Ruby, Coomassie Blue)
Dyversity compatible	Direct analysis of GLP secure images using the Dyversity unique capture system

Dymension 3 Specifications

Component	Description
System	Software for the rapid analysis of 2D protein spots between samples containing replicate gels, stained with visible or fluorescent dyes, and the analysis of multi-stained fluorescent gels
On screen views	Main pane and secondary panes for viewing replicates and samples. Syncronised zoom with intensity autoscale
Image processing	Automatic and precise image warping with vector view. Manual warp editing. Automatic background subtraction and noise filtering. SYPRO® Ruby Crystal filter
Spot detection	Automatic spot detection. Region of interest option. Gaussian spot modelling option for non-multiplexed analysis
Speed of spot detection	3x10 Mbyte images in eight seconds
Automatic spot matching	Generates averaged gel image and performs average gel warping. Matches spots
Spot editing	Spot detection with user adjustable parameters. Spot editing, filtering and normalisation
Image calibration	pl and MW ladder calibration. Protein list assignment of spots with known identity, pl and MW
Data visualisation	Interactive process flow diagram. Histogram (brightness and contrast). Main pane and secondary panes for multi-stained gel sets, replicates and samples. Bar chart. 3D spot profile. Table of spot matching results. Scatter plot. Correlation plot.

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