Image Analysis
An image analysis enables you to analyze simple shapes based on their gray values. For example, you can automatically count and classify particles in the sample according to their size or color.
Setting up an image analysis consists of the following steps:
- Classifying measurements
- Specifying the region of an image to be analyzed
- Configuring object detection
- Automatically correcting object detection
- Manually correcting object detection
- Defining values to be measured
- Previewing measurements
You are guided through these steps using the Image Analysis Wizard.
An image analysis can be run as follows:
- Interactively
- Automatically
When run interactively, the user can adjust the settings in each of steps 2-5 if enabled in the measurement definition. Since this mode requires a good knowledge of the sample and the software, it is typically used by supervisors in Free Mode.
When run automatically, the user cannot adjust any settings. The interaction is limited to acquiring or selecting the image and saving the analysis results. This is typical for inclusion in a job template. In this case, it is common to assign the image analysis to a macro and insert the macro into the template rather than the image analysis itself.
See also
Creating an Image Analysis Setting
To be able to automatically analyze a sample you first have to create a new image analysis or modify an existing one.
- You have opened an image and the Image Analysis workbench is selected.
- In the Image Analysis tool, click
to select a default setting file. - Click
to save the file in the Archive under a new name. - Click Setup Image Analysis.
- The image analysis wizard opens, see Image Analysis Wizard.
- Complete all the steps of the wizard and click Finish.
- You have created an image analysis setting. You can now run the image analysis in Free Mode, use it in a job template, or execute it with a macro.
See also
Running an Image Analysis
Image analysis can be run as follows:
- An image is displayed.
- The Image Analysis workbench is selected.
- Under Settings File select the desired image analysis file.
- If you are in Free Mode, click Analyze. If you are in Job Mode, go to the first step of the analysis.
- In Free Mode, you can change the parameters of every step where the Interactive checkbox was activated during setup. In Job Mode, you can change the parameters of every step that is not set to run silent. The rest of the image analysis is performed automatically.
- If you have selected a settings file that you created from a machine learning or AI model, some parameters of the image analysis are already predefined and cannot be changed, e.g. the number of classes and the segmentation method.
- The results of the image analysis are displayed in the image and a results table.
Analysis Tab
The Analysis tab is displayed at the bottom of each step of the Image Analysis Wizard.
The functionality of the tab is also displayed for every analyzed image opened in ZEN core (tab is called Image Analysis Options in that case).
It enables you to adjust the following global settings:
|
Parameter |
Description |
|---|---|
|
Show Objects |
Shows/hides the detected objects in the image |
|
Fill |
|
|
Opacity |
Adjusts the transparency of detected objects This only has an affect if Show Objects is activated. |
|
Show All Classes |
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Object Classification |
Only visible, if you have executed an object classification, see Using an Intellesis Object Classification Model for Image Processing. |
Operator Workflow - Counting Cells (Loaded Images)
Operator workflows are designed by Supervisors. In the following you see the operator workflow Counting Cells (Loaded Images), which allows to count fluorescently-labeled nuclei that can serve as a proxy for the cell number.
|
Tasks |
Description |
To Do |
|---|---|---|
|
Form |
The input form ZEISS Cells is provided. The form is displayed in the report. |
The default form is displayed. To change the form, in the Form Selection tool, select the form, see Form Selection Tool. Fill in relevant data according to your sample. |
|
Load File |
Load images you acquired earlier. |
In the Load Multiple Image tool, load images from disk to display them in the Center Screen Area, see Load Image Tool. Loaded images have the fluorescently-labeled nuclei as first channel. |
|
Image Segmentation |
Generate one mask for all nuclei per cell. |
Generate masks for nuclei, which are then counted, see Automatic Segmentation. To separate neighboring nuclei use a separation tool, e.g. Watersheds. If a large part of the image is selected initially, use background subtraction. |
|
Region Filter |
Results are refined based on area and circularity of the objects. |
To refine the selection to limit the analysis to one object or nucleus per cell, use region filters for area and circularity, see Region Filter. |
|
Measurement Data |
Check the results based on the previously conducted image analysis. The results are displayed in a table. |
To select an object, click a value in the table, and to check the size of a certain object, click the object in the Center Screen Area. For more information, see Measurement Data Tool. |
|
Report |
Creates a report document, see Reports. You can print the report. The report contains the following information:
|
For your documentation, you create a report. |
Image Analysis Workbench
This workbench enables set up and perform an image analysis. For example, you can automatically count and classify particles in the sample according to their size or color.
See also
Automatic Measurement Tool
This tool enables you to set up and perform an automatic image analysis.
|
Parameter |
Description |
|
|---|---|---|
|
Settings File |
Displays the selected settings file. |
|
|
– |
|
Opens a dialog to select your image analysis setting. |
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– |
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Saves the current setting to the Archive. |
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Class tree |
Displays a preview of the classes to be analyzed. |
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Setup Image Analysis |
Opens the Image Analysis Wizard to configure the image analysis. |
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Analyze |
Runs the selected image analysis. |
|