Direct Processing Tool on Acquisition Tab

Add Function

Adds another processing function to the pipeline.

Remove Function

Removes the currently selected processing function from the pipeline.

Pipeline

Displays a list of containers for possible processing functions. To set the function for the currently selected container, use the Processing Function dropdown list.
The functions in this pipeline are executed one after the other in the sequence as given here. You can change the position of a function in the pipeline via drag & drop.

Processing Function

Selects the processing function you want to use for Direct Processing for the currently selected container of the pipeline. Depending on your experiment, microscope, channel settings and licenses, a particular processing function is already preselected by default.

Parameter Section

In this section you have different parameters, depending on the selected Processing Function. For more information, see:

• Airyscan Joint Deconvolution Parameters
• Airyscan Processing Parameters
• LSM PLus Processing Parameters
• ApoTome RAW Convert Parameters
• Deblurring Parameters
• Deconvolution Parameters
• Denoise Parameters
• Extended Depth of Focus Parameters
• Intellesis Denoising Parameters
• Linear Unmixing Parameters
• Stitching Parameters
• Unsharp Mask Parameters
• Lattice Lightsheet Parameters
• SIM Processing Parameters
• Apotome Plus Parameters
• Lightfield 4D Processing Parameters

Adjust per Channel

Only visible for some functions and only if your experiment contains more than one channel.

Activated: Opens a list with the channels to allow an adjustment of each parameter for each individual channel. For every channel you also have the following options:

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Process Channel

Processes this channel according to the set parameters.

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Skip Channel

Skips this channel when processing. This channel will not be in the output image.

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Copy Channel

This channel is copied into the output image without processing.

Use Advanced Settings

Only visible if you have selected Deconvolution or Apotome Plus.
Activated: Enables the dropdown menu to load an advanced setting.

Load Setting created in the Deconvolution function

Only available if Use Advanced Settings is activated and Deconvolution is selected.
Selects advanced settings which were created in the image processing function Deconvolution (adjustable).
Note: Currently Direct Processing only supports settings configured in the Deconvolution tab of the function, some settings on the PSF tab such as spherical aberrations correction cannot be used in Direct Processing.

Load Setting created in the Apotome Plus function

Only available if Use Advanced Settings is activated and Apotome Plus is selected.
Selects advanced settings which were created in the image processing function Apotome Plus (adjustable).
Note: Currently Direct Processing only supports settings configured in the Apotome Plus tab of the function, some settings on the PSF tab cannot be used in Direct Processing.

Output

Only visible if Show All is activated.
Displays options to adjust setting for the output image(s).

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Output Folder

Displays the path where the processed image is saved. Make sure that a shared folder is selected where both the acquisition and the processing computers have access to.

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Use Output Folder from Auto-Save

Activated: Synchronizes the output folder for Direct Processing with the folder in the Auto Save tool. The Output Folder can only be changed by editing the Folder in the Auto Save tool respectively. If you have opened a ZEN Connect Project, the folder in the Auto Save tool is automatically set to the folder where the ZEN Connect project is saved.

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Create Sub-folders Automatically

Activated: Creates sub-folders in the output folder. All processed images end up in a new folder named with the current date.

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Define File Naming

Defines the filename of the processed image. Default: processed.czi.

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Use Original Name with Suffix

Activated: Uses the name of the file as it was acquired and adds the defined file naming as a suffix.

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File Name Preview

Displays a preview of the name of the processed acquisition image.

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Remove Acquired Image after Processing

Activated: Keeps only the processed image and deletes the acquisition image after processing.
Deactivated: Keeps both the acquired and processed image.

Handling of Processed Image

Only visible if Show All is activated.
Selects if/how the processed image should be displayed here on the acquisition PC.

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Do Not Open Automatically

The processed image is not opened automatically.

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Display in Split View

The processed image is displayed in a splitter document together with the acquired image as soon as the first image data is processed.

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Only Open Final Image

The processed image is displayed after processing is completed.

Process On

Only visible if Show All is activated.
Selects where the processing of the image takes place.

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This PC

Selects the option to process the data on this PC, i.e. the PC used for the acquisition.

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Remote PC

Selects the option to connect to a separate (remote) processing PC for processing your data and displays an additional parameter to configure the connection.

Connected Processing PC

Only visible if Remote PC is selected.
Displays the status of your connection to a processing computer, for example to which PC you are connected and what the progress of your job is. If you are not connected to a PC, you can edit your connections here.

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Edit Connection

Opens the dialog which lists all the connected PCs that are ready to receive remote processing requests.