ZEISS Microscopy Knowledge Base
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ZEISS Microscopy Knowledge Base

Image Analysis Wizard

This wizard guides you through the setup of an image analysis. The following basic controls enable you to move through the steps:

Parameter

Description

Next

Moves on to the next step of the wizard.

Back

Moves back to the previous step of the wizard.

Cancel

Cancels the wizard. No changes are applied to your settings.

Finish

Saves the setup and the changes based on your progress and closes the wizard.

Classes

Difference in Job Mode

The available functionality of the individual steps can differ between the wizard in Free Mode and the steps that can be added in Job Mode, e.g. the Interactive checkbox is not visible in Job Mode.

In this step you can define the classes into which the measured objects in the image are divided.

Parameter

Description

Interactive

Activated: The measurement frame definition can be changed interactively while the analysis setting is run.

Class List

Displays the defined classes. If you create a new analysis setting, a predefined set of classes is created automatically.

Each class also contains a summation class (not displayed in the class list). Each class contains the individual regions belonging to that class and in the class result table the defined measurement features for each individual object are displayed. The summation class on the other hand concerns all the objects belonging to the class. The corresponding result table contains "statistical" features such as the object count or the mean intensity of all objects belonging to the class.

Add Class

Adds a new individual class to the list on the base level.

Add Subclass

Adds a new subclass to the selected class.

Remove Class

Deletes the selected class from the list.

Name

Defines the name for the selected class in the list. Note that you must not use the name Root for one of your classes as this a reserved keyword.

Channel

Selects the channel that is used for image segmentation of the selected class in the class list.

Object Color

Selects a color to mark the objects of a class.

Random

The objects found by the analysis will be colorized randomly.

Fixed

Selects the fixed color to mark the objects of a class.

Frame

Difference in Job Mode

The available functionality of the individual steps can differ between the wizard in Free Mode and the steps that can be added in Job Mode, e.g. the Interactive checkbox is not visible in Job Mode.

In this step you can define one or more measurement frames. Only the area within the measurement frames gets analyzed. You can also define how the analysis treats objects that are cut by the border of the image or the frame.

Parameter

Description

Interactive

Activated: The measurement frame definition can be changed interactively while the analysis setting is run.

Black mouse cursor arrow on white background
Select Frame

Enables you to select already created measurement frames. To select a measurement frame, click inside it. To select several measurement frames, press Ctrl and click inside the desired measurement frames. Once you have selected a measurement frame, you can change its size.

Draw Rectangle

Enables you to create a rectangle as a measurement frame in the current image.

Draw Circle

Enables you to create a circle as a measurement frame in the current image.

Draw Contour (Polygon)

Enables you to create a contour as a measurement frame in the current image.

Remove All Frames

Removes all drawn-in measurement frames in the current image. To delete single frames, select them and press Del.

Maximize Circle

Activated: Maximizes the drawn-in circle to the full image size. In the case of rectangular images the circle is adjusted to the shorter side.

Center Circle

Activated: Centers the drawn-in circle to the full images size.

Mode

Selects how the measurement frame should be applied. Note that this behavior is only applied when running the analysis (interactively) and not during the setup. The setup always uses the Cut at Frame mode. The following modes are available:

Inside Only

Measures only those objects, that are lying completely within the measurement frame. Objects that are touching the frame or are intersected by the frame are not analyzed.

White square with blue inner square containing scattered blue irregular spots and gray translucent blobs around it

Cut at Frame

Measures all objects that are lying within the measurement frame. Objects that are intersected by the measurement frame are measured precisely up to the measurement frame.

White square with blue inner square filled with many blue irregular spots and gray translucent blobs overlapping the edges

Left

Sets the starting point for the frame on the X axis in pixels.

Top

Sets the starting point for the frame on the Y axis in pixels.

Width

Sets the width of the frame in pixels.

Height

Sets the height of the frame in pixels.

Color

Selects the color of the frame.

Show Frame On Analyzed Image

Activated: Displays the frame on the image after the analysis has run.

Interactive Segmentation

Difference in Job Mode

The available functionality of the individual steps can differ between the wizard in Free Mode and the steps that can be added in Job Mode, e.g. the Interactive checkbox is not visible in Job Mode.

In this step you can post-process the segmented objects interactively. You can modify the results of the automated segmentation when you analyze your image data. Note that during the setup of the analysis (via Setup Image Analysis in Free Mode), the segmentation is only performed on the area visible in the viewport. If you enter the interactive analysis or are in Job Mode, the image will be fully segmented.

Parameter

Description

Interactive

Not available for Technical Cleanliness Analysis.
Activated: The segmented objects can be post-processed interactively while the analysis setting is run.

Class List

Not available for Technical Cleanliness Analysis.
Selects the class whose objects you want to process.

Edit Region section

Parameter

Description

Draw

Enables you to draw new objects of the selected class.

Erase

Enables you to erase parts of an object. While pressing the left mouse button, outline the parts of the object that you want to erase. Right-click to erase these parts of the object.

Cut

Enables you to separate connected objects. While pressing the left mouse button, draw in the separation line between the objects. Right-click to cut the objects.

Merge

Enables you to connect objects. While pressing the left mouse button, outline the parts of the object that you want to merge. Right-click to merge the objects.

Fill

Fills a hole. To fill a hole, left-click on the hole. If a selected object completely surrounds another potential area, then the enclosed area is also included (Blue-outlined, diagonally hatched amorphous blob with a larger blue-ringed interior hole and blue square label 2).

Two side-by-side striped blobs labeled 1 and 2; left shows a small unoutlined hole, right shows the hole outlined in blue.

Remove

Enables you to remove a drawn in object by clicking on it.

Remove All

Deletes all drawn objects.

Draw Rectangle

Enables you to add a rectangular object or cut a rectangular region from an object.

Draw Circle

Enables you to add a circular object or cut a circular region from an object.

Draw Contour

Enables you to add an object or cut a region from an object.

Draw Contour (Spline)

Enables you to add an object or cut a region from an object.

Draw Active Contour

Enables you to add an object or cut a region from an object.

Draw Polyline Region

Enables you to add a line-object.

Draw Point

Enables you to add a point object.

Region Growing section

For the module Technical Cleanliness Analysis, only Undo and Redo are available.

Parameter

Description

Mode

Expands or reduces the size of an object based on the brightness of surrounding pixels

+

Click on areas in the image you want to add to the selected object class.

-

Click on areas in the image you want to remove from the selected object class.

Intensity

Sets the tolerance value for the intensity. The tolerance value specifies how much the intensity of a pixel may deviate from the average intensity of the selected object in order to still "grow" to become part of the object. A higher value means that more pixel values similar to the selected one are included. A lower value means that only the exact pixel value selected is included.

Color

Only active if your input image is a color image.
Sets the tolerance value for the color. The tolerance value specifies how much the color value of a pixel may deviate from the average color value of the selected object in order to still "grow" to become part of the object. A higher value means that more colors similar to the selected one are displayed. A lower value means that only the exact color selected is displayed. The comparison is based on the RGB (red green blue) colorspace.

Fill

Fills holes that are created during region growing.

Activated (Blue-outlined, diagonally hatched amorphous blob with a larger blue-ringed interior hole and blue square label 2): If a detected object completely surrounds another potential area, then the enclosed area is also included.
Deactivated (UI panel listing Min. Object Size, Min. Hole Size, Fill all Holes and On/Off notes on filling holes in segmented objects): Only the detected object is included.

Two side-by-side striped blobs labeled 1 and 2; left shows a small unoutlined hole, right shows the hole outlined in blue.

Undo

Undoes the last action.

Redo

Restores the last undone action.

Post Processing section

Only visible for images with a size smaller than 10000 x 10000 pixel.

Parameter

Description

Region Filter

Reapplies the region filter you defined in the previous step to the post-processed image.

Results Preview

In this step you see a preview of the measurement results. The results table contains only the measurements performed in the current view port. These results may differ from the actual results when the complete image analysis is performed. This increases the performance during the setup.

The results in the table depend on the settings you made in the Feature step. The table contains all selected features for the highlighted class/classes. Click on a row of the table to highlight the corresponding object in the image or vice versa.

The following controls are only available in Free Mode:

Parameter

Description

Class List

Select the class for which you want to see the measured features.

Highlight Box

-

Color

Sets the color of the highlight box surrounding the selected object in the image.

-

Line Width

Sets the line width of the highlight box around the selected object in the image.

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