Image (Context Commands)

Add Attachment

Append an arbitrary file to the currently opened image document. The Select Attachment window appears, where you can specify the appended file.

Add Profile Line

Inserts a new profile line.

Add this Point to ND Acquisition

Appends a line to the current multipoint experiment table including the PFS offset.

Clear All Objects

Removes all vector objects from the current image.

Clear All Objects and ROIs

Erases all vector overlay layers of the current image i.e. annotations, measurement objects, ROIs.

Colorize Binary by 3D objects, Colorize by 3D objects

Having a Z-stack image and a 3D binary. This command colorizes the 3D objects to easily determine if two neighboring objects are connected or not. This command is available on a context menu over Volume View and Slices View.

The 3D binary is created by one of these commands:

Colorize Binary Objects

This function displays the binary objects in several different colors. The algorithm is optimized so that two neighboring objects would never display in similar colors.

Connect 3D Objects in Binaries

(requires: Standard)

Connects Z-stack slices of 2D binary objects into 3D binary objects. It equals the Binary > Connect 3D Objects in Binaries command and appears in the context menu when the image is displayed in Volume View.

Copy Binary

This function copies current binary image (in case of ND) from selected (visible) layers into clipboard. The copied binary layers can be inserted into another image or as a new image.

Copy Binary Layers

The function copies binary layers into the clipboard. The layers can be pasted into different documents.

Correlation Properties...

Displays the Correlation Properties dialog window used for defining the correlation view.

Apply

Applies the current correlation settings without closing the dialog window.

Cancel

Discards all the changes and closes the dialog window.

Channels

Set between which channels will the correlation be computed.

Correlation Range

Changes the correlation range (minimum and maximum values). Click Auto range... to determine a proper range automatically.

Help

Displays this help page.

Keep color scale in view

If checked, the color scale stays in view when the image is zoomed in.

OK

Confirms the settings and closes the dialog window.

View Method

Select a correlation method:

Binary Objects - computes the Pearson's correlation coefficient for each binary object.

Neighborhood - Pearson's correlation coefficient is computed for a square neighborhood of each pixel. Define the neighborhood size in pixels using the spin box.

Pixel Deviations - is calculated as a covariance per pixel.

Correlation View

Turns the Pearson's correlation on and off. It is used to visually interpret the relation between two image channels and to see which areas in the image are correlated.

Start by thresholding your image (see: Thresholding) to determine the areas where the correlation will be calculated. Then define the channels and method in the Correlation Properties dialog (Correlation Properties...) and confirm the settings by clicking OK. Now run this function to calculate the correlation.

Hovering over a thresholded area shows the Pearson's correlation value on the bottom right side of the image window. It takes values from -1 to +1 (default Correlation Range), where -1 is a total negative linear correlation, 0 is a no linear correlation and 1 is a total positive linear correlation.

Display User Events

Shows/hides information about user events if they are available.

Edit Points

This command is used for vector object editing.

Find this Point in Paired Document

If two images have matching XY coordinates, this function can be used to locate the position in one image inside the other one.

Move this Point to Center

Centers the XY stage to the selected point.

Move Z to this Position

Moves the stage(s) to a specified Z position.

ND Info Properties

Displays a dialog used for customizing the shown ND information.

Object Visibility

Sets visibility of the currently selected annotation/measurement object(s) over time.

Clear Selection

Clears the frame selection.

Finish

Applies the visibility and closes the settings window.

Help

Opens this help page.

Invert Selection

Inverts the frame selection.

Select All Frames

Selects all frames of the image.

See Working with the Measurement and Annotation Objects.

Open Attachment...

Opens the file attached to the currently opened document.

Open File Location

Opens the current image in Organizer ( View > Visualization Controls > Organizer ).

Paste Binary Layers

The function pastes binary layers from clipboard into current document. Clipboard must contain some binary layer.

Paste Objects

This function inserts all vector objects that are currently in the application clipboard to the current image. Some vector objects must have been copied to the clipboard previously.

Remove Attachment

This function removes the attached file.

Rescaling Method

Sets the selected type of picture rescaling method.

Reset All to Defaults

This function resets all changes made in the volume view into default.

Reuse > Reuse Camera Settings

Sets the camera settings to match the settings of the specified image file. The *.TIF, *.ND2 and *.JP2 file formats are supported. This function is invoked on the context menu in Opened Images and Auto Capture Folder control windows.

Reuse > Reuse Device Settings

Loads device-related metadata from an image file and sets the connected device(s) accordingly. The *.TIF, *.ND2 and *.JP2 file formats are supported.

Reuse > Reuse ND Setup

Sets the ND setup to match the settings of the specified ND image file. The *.TIF and *.ND2 file formats are supported. This function is invoked on context menu in 'Auto Capture Folder' and 'Opened Images' control windows and also on the 'Reuse' button in 'Image Properties' dialog box.

Reuse > Reuse Optical Configuration

Optical configuration is taken from the image and is reused.

ROI Properties

This command opens the ROI Properties dialog window where visual parameters of the ROIs can be set.

Save Attachment As...

Saves the attached file to a custom location.

Select All Objects

Selects all vector objects.

Set Document as Uncalibrated...

Removes the current image calibration. The image becomes Uncalibrated.

Show Binary Objects ID

This function displays/hides ID labels of the binary objects.

Show LUTs Intensity Range

Shows or hides the LUT visualization bar. LUT visualization bar is overlaid on top of the image.

Show ND Information

This function displays summarized ND information (information about the current frame of an ND2 document or live image).

Show Physical Zoom

Displays value of physical zoom (real magnification of the sample) in a box in the top left corner of the image. To hide the box, right-click on it and select Hide Physical Zoom.

Note

Correct monitor calibration is required by this function to work correctly. See Monitor Calibration.

Show Scrollbars

Turns on/off visibility of the scroll bars when the image is zoomed in.

Show Thumbnail of Merged All Channels

Sets the option whether the sub-view with all channels should be present in the Split Components viewing mode.

Show Thumbnail of Merged Custom Channels

Sets the option whether the Custom sub-view should be present in the Split Components viewing mode.

Toolbars

This function quickly changes the appearance and behavior of image toolbars. The same options are accessible in program options.

See Appearance Options.

Use all XY locations as preview in XYZ Overview

All multipoints present in the image are shown in the preview of the XYZ Overview panel.

Use as preview in XYZ Overview

Currently selected multipoint is shown in the preview of the XYZ Overview panel.

View Channel in Color

A single channel of an image can be observed as gray or colored. This function toggles between these two modes. The setting is applied to the current image only.