Project and Image Management

Within a ZEN Connect project, in the ZEN Connect tree view, you manage your data in a project structure tree combined with the viewer. Before acquiring or importing any images, you need to create the ZEN Connect project. Only within a ZEN Connect project, you can use all ZEN Connect functionality.

You can open only one ZEN Connect project at a time.

1. You have set up the sample on the microscope.

1. In the ZEN Connect tool, click Create.
2. The New Document Dialog dialog opens.
2. In the New ZEN Connect Project Setup area, select the Project Path where you want to store the ZEN Connect project file.
3. Select the relevant data to configure the ZEN Connect project. If you select the holder/carrier now, you can change it later. Note: If you change the holder/carrier after a S&F calibration, the S&F calibration needs to be redone.
4. Click on OK.
5. The ZEN Connect project is created with the project file name <Projectname>.a5proj. Note that all new images are saved in the subordinated folder <Projectname_data>. You can always check the path on the Acquisition tab in the Auto Save tool. Alternatively, right- click on the project container in the Center Screen Area and select Open Containing Folder.
6. In the Image View, the sample holder is displayed.
   
7. In the ZEN Connect tool, the empty ZEN Connect project is displayed. Here, the structure of the ZEN Connect project will be displayed as soon as you acquire or import images. In the folder on your computer, the ZEN Connect project file <CWS project name>.a5proj is generated. A <ZEN Connect project name>.a5lock is generated to prevent more than one user to work on the project at the same time. It is generated any time you load a ZEN Connect project.
8. At the bottom of the Image View, a scale bar with size, the width of the field of view (FOV), and scaling is displayed.
9. You have created a ZEN Connect project.
5. Acquire an image.
6. In the Project View, a new session node is created, and each acquisition is displayed.
   
7. In the Image View, all images are displayed. They are signed with a colored frame (blue: normal image, red: selected image).
6. When you close the project or the software, you are prompted to save the project file.

For information on setting up holders and carriers, see Selecting and Clearing Carrier/Holder.
For information on the ZEN Connect tool, see ZEN Connect Tool.

You can load any of your ZEN Connect projects to continue with your work. You can also load existing ZEISS Atlas 5 projects.

Open first the ZEN Connect project before performing a S&F calibration.

1. You have created a ZEN Connect project, or a ZEISS Atlas 5 project is available. ZEISS Atlas 5 projects belong to the ZEISS ATLAS 5 software. ZEN Connect supports these formats.

1. Select File > Open, navigate to the ZEN Connect project and open it.

1. In the ZEN Connect Project View, the current state of the Connect project is displayed. In the Image View, the sample holders are marked, and previously acquired images are displayed. The current stage position is marked with a cross hair. If you want to acquire additional images to the project, align the new session with the existing data.

See also

• Opening or Deleting a ZEN Connect Project from ZEN Data Storage

You can import simple images, such as camera images or more complex images, such as a light microscope image with overlays, into your ZEN Connect project.

You can use an imported image as a backdrop to navigate the region. You can correlate imported images with sample holder marks, e.g., fiducials or other images through the alignment process. The imported image is displayed according to its position in the Layers View along with any other image in the project.

The metadata of .CZI-images are read natively and are also imported.

1. You have loaded a ZEN Connect project.

1. In the ZEN Connect tool in the on Project View , right-click a session and select Add image. Alternatively, for the Import button, select Add image. If you want to add an image from ZEN Data Storage (without downloading it), right click in the Imported Data and select Add image from storage.
2. You are prompted to select the image you want to add.
2. If you want to import the image as a background image (at the lowest level of the project structure), activate the Background Image checkbox.
3. You also have the option to copy the image in a subfolder of the file where the project data is stored before adding it to your project. Activate Copy files.
4. Click on Open.

1. The image is imported to your ZEN Connect project.
2. In the Project View, it is displayed in the tree, subordinated to Imported Data.
3. If Shuttle & Find-calibration is available for the image and the image is at least in one session in the ZEN Connect project, the image is placed in the Image View according to the Shuttle & Find stage position. Take care that you select the correct sample holder when importing an S&F-calibrated image. The correct sample holder is the same sample holder that was used during acquisition.
4. If no Shuttle & Find data is available, the image is displayed centrally in the FOV of theImage View.

To add an open image to a project, see Adding an Open Image to the ZEN Connect Project, and to add a dataset, see Adding Datasets when Adding Images.

Additionally, you have the following options to import data in your ZEN Connect project:

• Importing Data
• Importing Third-party Images
• Importing a SmartFIB Stack into ZEN Connect
• Saving an Image to ZEN Data Storage
• Importing Non Image Data

Note: If you import an Airyscan image, ZEN Connect displays only the raw data and not the calculated Airyscan. Such images should be processed before you add them to ZEN Connect. If you want to add an unprocessed Airyscan image, a warning will appear asking if you want to continue.

Note for z-stacks: When you use the Global Z slider and are beyond the range of a certain image, only a frame for this image is displayed to show where the image is positioned.

1. You have loaded a ZEN Connect project.
2. You have an open image (which is not part of the project).

1. Click on File > Add to ZEN Connect Project.
   Alternatively, you can use the button in the tool bar which is available if you customize your application by clicking on Tools > Customize Application... > File > and double click Add to ZEN Connect Project. This button is automatically available in the tool bar for all users of the EM Processing Toolbox module.

1. The image is added to your ZEN Connect project.

Additionally, you have the following options to import data in your ZEN Connect project:

• Importing Data
• Importing Third-party Images
• Importing a SmartFIB Stack into ZEN Connect
• Saving an Image to ZEN Data Storage

Note: If you import an Airyscan image, ZEN Connect displays only the raw data and not the calculated Airyscan. Such images should be processed before you add them to ZEN Connect. If you want to add an unprocessed Airyscan image, a warning will appear asking if you want to continue.

Note for z-stacks: When you use the Global Z slider and are beyond the range of a certain image, only a frame for this image is displayed to show where the image is positioned.

See also

• Adding an Image to the ZEN Connect Project

You can zoom images in and out of a field of view (FOV).

Zooming to

1. A ZEN Connect project is loaded.

1. In the Project tree View, right-click an image and select Zoom to. Alternatively, click on the Context menu button and select Zoom to.

1. The image is centered in the view space of the Image View.

Zooming to 100%

1. A ZEN Connect project is loaded.

1. In the Project tree View, right-click an image and select Zoom to 100%. Alternatively, click on the Context menu button and select Zoom to 100%.

1. The image is zoomed in the view space of the Image View to 100%.

You can remove images from your ZEN Connect project. Images you acquired and added to the project, you can also delete permanently from the disk.

1. You have loaded a ZEN Connect project.

1. In the Project view or in the Layer view, select the images to remove.
2. Right-click the image, and select Remove data. Alternatively, click on the Context menu button and select Remove data. If you want to remove an acquired image, you are asked if you also want to delete it from the disk.

1. The images are removed from the ZEN Connect project. If you remove all images from the folder, the folder is removed as well. Removing data cannot be undone.

See also

• ZEN Connect Tool

1. You have loaded a ZEN Connect project.

1. In the Project View or in the Layers View, select one or more images you want to open, and right-click Open image(s) in ZEN. Alternatively, click on the Context menu button and select Open image(s) in ZEN. Additionally, you can also simply double click on an image in the Project View or in the Layers View.

1. The image is opened in ZEN and displayed on a separate tab.

ZEN Data Storage

If you have opened a project from ZEN Data Storage, you can also open an individual image this way. The image is then downloaded and each change is not updated in the viewer and the project until you upload the image again. For information on uploading an image to the data storage, see Saving an Image to ZEN Data Storage.

You can locate an image on your computer.

1. You have loaded a ZEN Connect project.

1. In the Project View or in the Layers View, right-click an image and select Show in Explorer. Alternatively, click on the Context menu button and select Show in Explorer.

1. The explorer opens and the folder with the selected image is displayed.

In the Layers View, you can move images over and under other images, or hide them completely. In the Project View, you can hide images.

1. You have loaded a ZEN Connect project with at least two images.

1. To change the image order, in the Layers View, move the image by dragging it up or down.
2. In the Image View, the changed order is immediately visible.
2. To hide the image from the ZEN Connect project, in the Layers View, activate or deactivate the image by clicking the Eye icon on the right of the image name. Alternatively, in the Project View, right-click Show/Hide or click on the Context menu button and select Show/Hide.

1. The results of your changes are displayed immediately in the Image View.

See also

• ZEN Connect Tool

To organize your work, you can start a new session within your ZEN Connect project any time.

1. You have loaded a ZEN Connect project.

1. In the ZEN Connect tool, click on the Context menu button and select New session.
   Alternatively, click on the New Session button.

1. A new session is activated. As soon as you acquire a new image, a new session node is created, and the new image will be subordinated.
   

See also

• ZEN Connect Tool

In ZEN Connect you can switch between two different view modes for your projects. The default is the carrier/ holder view mode, where the coordinate system of the correlative workspace is aligned with the screen and images of the current system/ session might be rotated. The second is the stage centric view mode, where the coordinate system of the current session is aligned with the screen and the carrier/ sample holder as well as other sessions might be rotated.

1. You have opened a ZEN Connect project.

1. In the button bar below the Image View of the correlative workspace, click on the button for the carrier/ holder or the stage centric view mode.

1. The view is changed according to the selected view mode.