1.2 Scatter plot: illustrates the expression differences between two gel images
1.3 Expression profil rollup indicating project wide spot intensity
3.1 Invitation to import the license
3.2 Initial license file is imported
3.3 Send your registration request
3.4 Enter your registration key or load a full license file
3.5 Preferences: Memory
4.1 The project manager
4.2 The Gel Image Manager
4.3 Image Import Dialog
4.4 The gel image properties dialog, available when importing images into the pool, or by right click on an image thumbnail in the Project Manager.
4.5 Create a new gel image attribute, here a gel.
4.6 The gel image attributes dialog, accessable from the Project Manager, by choosing the Project
Gel Image Attributes. . . menu item.4.7 The project manager dialog
4.8 Creating a group
4.9 Details in project table
4.10 Image Fusion dialog
4.11 The job manager
4.12 The spot detection and quantitation dialog.
5.1 The Gel Image Pair View, also named Dual Image View, or, in short, Dual View
5.2 The tabs for controlling image visibility
5.3 The tool panel.
5.4 The icon bar of the Gel Pair View
5.5 The status bar of the Gel Pair View
5.6 The colors rollup
5.7 The overlays rollup
5.8 Button to temporarily hide all objects
5.9 The navigator rollup
5.10 The zoom rollup
5.11 The Expression Profile rollup. The columns are colored according to the replicate group. The black lines indicate the mean plus minus the relative standard deviation.
5.12 The 3D spots rollup
5.13 The pI/MW Calibration rollup
5.14 Setting the data source for pI/MW-Calibration
5.15 A dual channel image with and without background.
5.16 Visual background settings
5.17 The histograms dialog.
5.18 Preferences: Image preparation
5.19 A region of the dual channel image, before and after exact warp.
5.20 A region of the dual channel image, before and after global warp.
5.21 An image region after exact and after global warp
5.22 Setting match vectors.
5.23 Preferences: Match Vectors
5.24 Apply complete warping strategies at once
5.25 Group Warping Strategy
5.26 Chain Warping Strategy
5.27 Chained Group Warping Strategy
5.28 One-To-All Warping Strategy
5.29 In-Gel Standard Warping Strategy
5.30 The result of the visual comparison process.
5.31 How colors are combined in the dual channel image
5.32 The color schemes dialog.
5.33 The color schemes display.
5.34 The color schemes display for ratio mode.
5.35 Some predefined color schemes
5.36 A gel region shown in ratio mode.
6.1 The quantitation dialog.
6.2 The quantitation dialog for both gel images loaded in the Gel Image View.
6.3 The cursor position in pixel count in the Status bar
6.4 The same region with pixel based and model based spots.
6.5 Edit spots
7.1 A Dual Channel Image with Labels on the Proteome Map.
7.2 Delta2D tool panel with activated label tool.
7.3 A new label
7.4 The greek mode
7.5 The context menu for a label
7.6 The scout data attached to one label
7.7 Editing label formats
7.8 Labels colored according to isoelectric point, based on Scout data
7.9 Adjust details for scout based color coding of label elements.
7.10 Label selected spots with numbers
7.11 Pick list made from labeled spots
7.12 Label names and corresponding protein names in a spreadsheet
7.13 Translate Labels Dialog
7.14 Translated Labels
8.1 The quantitation table
8.2 The properties dialog of the quantitation table
8.3 Part of quantitation table, sorted on the fifth column
8.4 Automatic counting in the title bar of the correspondence table.
8.5 Editing a table row filter.
8.6 A filter that hides expression ratios between 0.5 and 2.
8.7 The scatter plot
8.8 Same region of four different gel images
8.9 A Region with Colored Spots. The color of a spot indicates on which sample(s) it is increased.
8.10 Choose Colors and Master Image
8.11 The expression profiles window
8.12 A Heat Map
8.13 The properties dialog of the quantitation table
8.14 Start analysis from the Quantitation Table
8.15 In this clustering you see an experiment with control (C1, C2, C4, C5) and treated (T1, T2, T3, T4) samples, made in triplicates. The clustering rediscovers the experimental setup, i.e. gel images with similar samples share a cluster. A sample forming a separate cluster would indicate an outlier for which closer inspection is advisable. Made using Pearson correlation as the similarity measure between images.
8.16 Spots with similar expression profiles are clustered together. Support Tree clustering with Euclidean distance.
8.17 Cutting a tree by a distance threshold. Use the slider to adjust the threshold.
8.18 Combined expression profiles in 12 clusters.
8.19 Result of applying t-tests (control vs. treated) to expression profiles. Profiles and images were clustered to better visualize differentially expressed proteins. P-values are based on 1000 permutations, false discovery rate is controlled to be 5 elements or less (with overall alpha=1%).
8.20 a): Expression profiles matching the template. b): Comparison between template (blue line) and matching expression profiles.
8.21 With Pavlidis template matching (PTM) you can specify a typical expression profile, e.g. one that increases with time.
8.22 a): Principal component analysis of 24 gel images in 3 dimensions. Parallels have the same color. The view can be rotated by dragging with the mouse. Again, replicates are placed close together. b): The same principal component analysis of 24 gel images, projected onto the first two principal components. Treated and control samples (reddish vs greenish colors) can be separated.
8.23 Principal component analysis of expression profiles in three dimensions. Differentially expressed spots were determined by t-test and highlighted orange and blue, respectively. Inset: First principal component.
8.24 The spot album report
8.25 The spot quantities report
9.1 Preferences: Image preparation
9.2 Preferences: Files
9.3 Preferences: Match Vectors
9.4 Preferences: Spots
9.5 Preferences: Labeling
9.6 Preferences: Tables
9.7 Preferences: Appearance
9.8 Preferences: Projects
9.9 Preferences: Memory
9.10 Preferences: 3D Spots
9.11 Preferences: License