Image Acquisition

With a very high number of experiments saved in the Experiment Manager (more than 500), moving from the Locate to the Acquisition tab takes a considerably long time. Delete redundant or no longer used experiments to avoid this lag time.

1. You have switched on and configured your microscope system and all components.
2. You have successfully started the software.

1. In the Left Tool Area, open the Acquisition tab.
2. In the Experiment Manager, click and select New from the dropdown.
3. A new experiment is created.
3. Enter a name for the experiment, e.g. "3-channel_experiment".
   
4. To save the experiment, click .

1. You have created a new, blank experiment. All other settings are now stored in this experiment. If you make changes to the experiment, an asterisk (*) after the file name appears. This means that the experiment was modified and not saved. Save your experiments from time to time to ensure that your settings are not lost.

Any experiment can be set as a startup default indicated by a symbol.

If you want to set an experiment as startup default, the following steps are necessary.

1. In the menu bar click on Tools > Options....
2. Click on Startup/Shutdown.
3. In the Experiment section, select Load Default Experiment from the drop-down list.
4. Click on OK.
5. The Options dialog closes.
5. Configure your experiment for startup default or select an existing experiment.
6. Click on Options and select Set As Start up Default.
   

1. The active experiment is set as startup default now and marked with the symbol.
2. This experiment is loaded when starting the ZEN software.

It is possible to generate an experiment template. This cannot be modified but used as a starting point for your acquisition.

If you want to generate an experiment template, the following steps are necessary.

1. Create an experiment.
2. In the menu bar, click on Help > About ZEN...
3. The About ZEN dialog appears.
3. Click on Show ZEN Information.
4. The Application Information dialog appears.
4. Open the Folders tab, scroll to the Experiment Templates entry, and double-click on it.
5. The folder Experiment Setups will open.
5. Export the experiment generated before into the Carl Zeiss\ZEN\Templates\Experiment Setups folder.
6. Create a descriptive name for the experiment template.

1. You have successfully created an experiment template.
2. It is possible to generate and save multiple templates.
3. To apply an experiment template, see chapter Applying an Experiment Template.

If you want to apply an experiment template as a starting point for your acquisition, the following steps are necessary.

1. The experiment template to be used has been created before, see chapter Creating Default Experiments as Templates Automatically.

1. On the acquisition tab, click on the options button and select New from Template.
2. The available experiment templates will be shown on the right side.
2. Click on the name of the appropriate template.

1. The selected experiment template will be loaded as starting point for the acquisition.

Using annotations you can highlight specific regions, add metadata or specific measurement information to images and movies. You can use the annotations within several workflows and functionality:

• For your own information, you can display metadata within images and movies.
• When working with Mean ROI view, you use the annotation functions to draw regions into the image.
• When analyzing images manually, you can record measurement results in the image.
• When exporting images or movies, you can add annotations that are visible in the export format of your images and movies.

The annotation tools are accessed via the Graphics tab or the Graphics Menu.

1. You have acquired or loaded an image or a movie.

1. In the Center Screen Area select the Graphics tab.
   
2. Select an annotation or a measurement and add it to the image.

Remove Annotations

1. Select the annotation in the image or in the Annotations/Measurements table, and press the Del key. Alternatively, right-click the annotation and select Delete.

Additionally, the annotations can be edited, rearranged, and formatted. For more information, see Editing Annotations in Images or Movies.

You can edit, rearrange and format annotations in an image or movie.

Edit Annotations

You can change the annotations type or the unit of the time or of the measurement.

1. To edit text in a textbox, double-click the textbox and change the text.
2. In the image, select the annotation and right-click to open the context menu. Select Format Graphical Elements.
3. The Format graphical elements dialog opens.
3. Edit the annotation and click Close to save.

Rearrange Annotations

1. Select the annotation with the left mouse button and drag and drop the annotation to another position.

Format Annotations

1. In the image, select the annotation and right-click to open the context menu. Select Format Graphical Elements.
2. The Format graphical elements dialog opens.
2. Format the annotation and click Close to save.

See also

• Adding Annotations to Images or Movies

ZEN offers the functionality to use a machine learning model trained for denoising directly during a continuous acquisition. Note that currently only models trained with ZEN are supported.

1. You have trained or imported a denoising model in ZEN. For more information, also refer to Intellesis Denoising. Note that in order to be able to train a model, you need the license for the AI Toolkit.
2. Docker Desktop is installed together with the denoising container and running.

1. On the Acquisition tab, set up your acquisition with the respective tools, e.g. Imaging Setup, Channels and Acquisition Mode tool. Note that the Acquisition ROI must have a frame size of at least 1024x1024 pixel! Depending on the chip size of your camera you have to check image size and binning to ensure that the frame size meets this requirement.
2. Your acquisition is set up.
2. In the Channels tool, activate Live Denoising.
3. The dropdown is activated.
3. In the dropdown, select the denoising model you want to use.
4. Denoising is now activated for your acquisition. Note that for widefield systems with a dual camera, only the first model will be applied to both channels.
4. Click Continuous.

1. You have started a continuous acquisition with simultaneous denoising.

See also

• Creating and Training an Intellesis Denoising Model