Analysis Tab

The Analysis tab is used to create a general analysis for any image.

• The Type group has a drop-down menu for specialized types of analysis. Select the type of analysis to apply and the Analysis tab for that application is opened. The last used parameters for that particular analysis type are used to create the new analysis.
• The Shapes group has tools for adding basic shapes to the image. The Add Rectangle and Add Ellipse tools are not available in multi-image mode. To use these Create tools, change the view to single image mode. All other Shape tools are available in multi-image or single image mode.
• The Edit group has tools for editing the shapes.
• The Auto-Adjust tool moves the selected shape(s) to surround a nearby area(s) of pixel intensity.
• The Background group has tools for defining the background.
• The Show options determine what is displayed on the image.

Adding Shapes

Shapes can be a rectangle, ellipse, or other shape drawn around some section of the image. Shapes can be quantified.

Click Features at the top left corner of the Display panel to toggle between displaying and hiding all features on the image. Features include Shapes, Bands, Lanes, Wells, Spots, Annotations, and more. Select specific features to display or hide in the Show group in each Analysis tab.

To add a shape:

1. Open the Analysis tab and choose the type of shape you want to add. There are several ways to place a shape on the image:
• Add Rectangle — Click the center of the feature in the image view. The rectangle automatically surrounds the feature.
• Add Ellipse — Click the center of the feature in the image view. The ellipse automatically surrounds the feature.

You can only add the auto shapes (Add Rectangle and Add Ellipse)to a single channel at a time. All other shapes will be added to all channels that are currently visible.

• Add Selection — Select a shape. Click the center of the feature in the image view where you want to add a shape. The selected shape is copied and added.
• Draw Rectangle — Click and drag from the top left to the bottom right to surround the feature.
• Draw Ellipse — Click the center of the feature and drag to the right or left to surround it.
• Draw Freehand — Click and drag the shape until it surrounds the area of interest.
2. Continue adding the selected shape until you have finished.
3. Click the Select button to end adding shapes (or press ESC).

Editing Tools

There are several tools for editing features on an image. To edit one or more features, first select the feature(s).

Selecting a feature

1. Click the Select button .
2. Click anywhere inside the feature that you want to select.
3. To extend the selection (select another feature), hold down CTRL and click anywhere inside the next feature you want to select.

You can also do a "sweep" selection by dragging a box around a set of shapes. Add to the selections using the CTRL key.

Select All

Click Select All to select all features on the image. Selection will include all shapes, labels, and any annotation you may have added.

Deselect All

Click Deselect All to deselect all selected features on the image (or click the image anywhere outside the selected features).

Invert Selection

Select a feature, then click Invert Selection to deselect the feature you selected and select everything else on the image.

Cut

Select the feature (or features) that you want to cut, then click Cut.

Copy

Select the feature (or features) that you want to copy, then click Copy.

Paste

Place the cursor where you want to place the copied or cut feature (or features), then click Paste.

Delete

Select the feature (or features) that you want to delete, then click Delete.

Duplicate Across Channels

Select the feature(s) that you want to duplicate on other channels, then click Duplicate . This copies the selected features on one channel and pastes them on all other channels.

Rotate

Select the feature that you want to rotate, then click Rotate .

Background

Three background subtraction methods are available for a manual analysis:

• Average
• Median
• User-Defined

None may be chosen, but signal will not be calculated.

Add-on analysis types have their own background subtraction methods. See one of these topics for more information about background subtraction in an add-on analysis:

• Background methods for blot and gel analyses (ie Western, MPX^™ Western, DNA Gel)
• Background methods for analyzing Plate and Grid based analyses (ie Plate, Plate Array, Grid, Grid Array)
• Background methods for analyzing the In-Cell Western analysis
• Background methods for a Small Animal Image analysis

Average and Median Background Methods

The Average and Median background methods will be discussed together, because they are the same except for using an average versus median.

User-Defined Background Method

The User-Defined background method finds the average pixel intensity within a shape or shapes placed by the user to calculate background. More information is provided below.

When to Use None

Unless data are going to be exported for analysis using a third-party software, do not choose None.

Signal will not be calculated if None is chosen, so the Total for each shape must be used in outside calculations.

Show Group

You can quickly remove all annotations and features on an image by clicking Features at the top of the Display panel on the right side of the application window.

• Shapes — Shows the shapes on image view. Exports and prints of the image view will show shapes when this Show option is checked.
• Labels — Shows labels of features on the image. Exports and prints of the image view will show labels when this Show option is checked.

1. To specify where to place the labels, click the arrow at the bottom right of the Show group.

   

2. This opens the Image View Show Options dialog.

   

3. Use the drop-down menus to select the position for the labels and what quantification value to display if Quantification is checked.
4. Click OK when you have finished.

• Quantification — A quantification value can be displayed on the image. Select from the drop-down menu in the Image View Labels dialog shown above.
• Local Background — Show local (Average or Median) background area used for shapes in the Image View.
• Text — Shows any text that you may have added on an image. Exports and prints of the image view will show text when this Show option is checked.

• Color Bar — Show a color bar on the single image view when only one channel is showing. The color bar is also shown on exports and prints of the image view.