Chapter 9
Preferences

9.1 Image Preparation

Figure 9.1: Preferences: Image preparation

Prescale

Scales larger images down to the given pixel count. Smaller images are not affected. Prescaling happens when images are loaded and is transparent to the user. Use this option to improve performance for large images. The scale factor for both images is determined by the first image loaded. The pixel count must be set to 50 at least.

Amplitude rescale

Enhances images by amplitude rescale when they are loaded. If this option is checked, the gray values of an image are rescaled linearly so that the darkest pixel becomes black and the lightest pixel becomes white.

9.2 Files

Figure 9.2: Preferences: Files

Multiple data locations

If this option is selected, the file chooser can remember to look for different types of data in different directories. This option may be useful if you want to store images and quantitation results in different directories, for example.

Remember separate data locations

If this option is selected, Delta2D will remember the storage locations for all different data types, even after it is closed and restarted. Otherwise, the file chooser will look for all types of data in the default directory after Delta2D is restarted.

Create backup files

If this option is selected, Delta2D will create a backup copy of overwritten files in the same directory.

9.3 Match Vectors

Figure 9.3: Preferences: Match Vectors

Match Vector Snap To Spot

If this option is selected, match vectors will snap to the nearest spot when they are moved around. This option can be temporarily toggled by pressing the control key while moving the match vector.

9.4 Spots

Figure 9.4: Preferences: Spots

Modeled Spot Shape Extent

The size of the spot boundaries will be reduced to the percentage defined here. Aplies only for the spot detections in the future and if the parameter Create Modeled Spots will be chosen.

Re-model Spots after Transfer

If this option is checked, while spot transfer the spot boundaries will be adjusted to the actual spots as they appear on the target image. Aplies only for spot transfers in the future and if the originally detected spots on the source image have been modelled.

9.5 Labeling

Figure 9.5: Preferences: Labeling

Label Snap to Spot

If this option is selected, labels will snap to the nearest spot when they are moved around. This option can be temporarily toggled by pressing the control key while moving the label.

Numbering of New Labels

If switched on, every new label created by a click in the Dual View is already filled with a consecutive number.

Prefix for Numbered Labels

Here you can define a prefix you would like to see in labels befor the automatically assigned numbers, e.g. "‘Spot"'.

9.6 Tables

Figure 9.6: Preferences: Tables

Show All Matching Spots

This options controls how spots behave when they have matching spots on other gel images and you want to hide them. If checked, matching has priority before hiding and these spots are not completely hidden. If not checked, hiding has priority and they are hidden without respect to possible matchings.

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Note:

This setting applies to the property hide in the context menu of spots in the Gel Image Pair View, the property hide in the Quantitation Table, and any filter in any tabular view.

Show Ratio of Spots as Fold Change

By default, the ratio of spots is shown as quotient of the two corresponding spots: if the relative volume of the second spot has the double size of the first spot, the ratio is 2, if its volume has half of the size, the ratio is 0.5. If you check this box, the ratio will be shown as fold change: double spot size means the ratio 2 as well, whereas half size will be shown as -2.

Show Ratio as Color

If this option is selected, a color coded icon is shown for ratios too.

9.7 Appearance

Figure 9.7: Preferences: Appearance

Model spot outlines

This option lets spots be modeled as an ellipse which has the same area as the spot.

Smooth Zoom

Normally, zooming in images magnifies with the whole image the single pixels, too. Thus, the more you zoom in, the more the image looks like covered with a grid. This option makes Delta2D smoothen the images in magnified state. This setting only affects the optical representation of images and no quantitative data at all.

Fill Selected Spots

If this option is selected, selected spots will be filled with transparent color.

Look-And-Feel-Chooser

Changes the outer appearance of Delta2D. Choose a Look and Feel of your taste.

9.8 Projects

Figure 9.8: Preferences: Projects

9.9 Memory

Figure 9.9: Preferences: Memory

Physical Memory (RAM):

shows the automatically detected amount of memory in your machine.

Currently Reserved:

This is the maximal amount of memory Delta2D reserves for its own use.

Reserve:

Here you can change the maximum of memory Delta2D should use. To apply changes of this setting, please restart Delta2D.

Recommend

Click on this button to change the setting to a recommended value, depending on the amount of memory detected.

Recommend (Nice)

This button changes the setting to a recommended value, depending on the amount of detected memory but considering other applications.

Keep Images in Memory

If this option is checked images are kept in memory after they are loaded. This is especially useful when working with a database pool. On the other hand side the system could run out of memory with big projects. This option will be applied only when new images are loaded.

9.10 3D Spots

Figure 9.10: Preferences: 3D Spots

Fixed Background color

Normally, the background of the 3D Rollup is determined by the color scheme used in the Gel Image Pair View. This setting allows you to determine the color of the background yourself: Simply check this check box and select a color with the now activated color picker.

Single View With Histogram Settings

Check this box to view the 3D representation of the single view with the histogram settings.

Single View as Wireframe Model

and

Dual View as Wireframe Model

If not checked, the 3D spots have an opaque surface, like in the gel image. Check this box to switch to a representation with a transparent surface; the spots will be shaped by lines describing the outline of the actual spots as shown in figure 5.12.

Separate Color Scheme

By default the colorization of the 3D spots in the Gel Image Pair View is exactly as described by the chosen color scheme in the Gel Image Pair View, considering not only the intensity ("height") of each pixel on each gel image, but also the ratio between the intensities. Check this box to colorize the spots only by intensity and not by ratio.

Fixed Size

By default, the 3D rollup shows only the selected spot, but in an optimized size; the spot will be scaled so that it fits best in the rollup. Checking this option turns off optimization so that the region shown in the rollup includes all spots existing in this area and will always have the same size, which you can specify (in pixels) in the field on the right.

Height Scale

lets you change the scaling of height, if e.g. your gel image has generally very high or very low contrasts and thus the spots appear to be very high or very flat in the 3D rollup.

9.11 License

Figure 9.11: Preferences: License

Import

This button allows to import a new license file. The file browser window will be opened to search for another license file. The current license file will be renamed to license.lfk.bak while the new license file will be stored with the name license.lfk, regardless of its original name.

Description

The description contains information about the kind of the license, where the license file is located, and some technical licensing details.