Parameter

Description


Options

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New

Creates a new Guided Acquisition setting. Enter a name for the setting.

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Rename

Renames the setting.

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Save

Saves a modified setting under the current name. An asterisk indicates the modified state.

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Save As

Saves the current setting under a new name. Enter a name for the setting.

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Import

Imports an existing setting.

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Export

Exports the current setting.

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Delete

Deletes the current setting.

Repeat Full Guided Acquisition Workflow

Activated: Displays parameters to repeat the entire workflow over time.

Cycles

Only visible if Repeat Full Guided Acquisition Workflow is activated.
Defines the number of repetition cycles for the workflow with the slider or input field.

Interval

Only visible if Repeat Full Guided Acquisition Workflow is activated.
Defines the minimum requested time between cycles with the slider or input field. The dropdown selects the time unit (minutes, hours, days).

Object Detection Dropdown

Only visible if Repeat Full Guided Acquisition Workflow is activated.
Selects which action should be taken for repeated iterations if no object are detected during the workflow.

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Keep Iterating if no Object Detected

Continues to iterate even if no objects are detected.

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Stop Guided Acquisition if no Object Detected

Stops Guided Acquisition if no objects are detected.

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Keep Acquiring Scenes without Analysis Findings

Only visible if your overview experiment contains a setup with multiple scenes.
Continues the acquisition also for scenes where nothing is detected by the analysis.

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Exclude Scenes without Findings in Following Iterations

Only visible if your overview experiment contains a setup with multiple scenes.
Only acquires scenes in subsequent iterations, if the analysis produced results.

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Exclude Wells without Findings in Following Iterations

Only visible if your overview experiment contains a setup with multiple wells.
Only acquires wells in subsequent iterations, if the analysis produced results.

Overview Scan

Defines the settings for the overview scan.

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Experiment

Selects the experiment setup to acquire the overview scan.

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Order

Only visible if your overview experiment contains a setup with multiple scenes or wells.
Selects in which order the individual scenes are acquired and processed. The following options are available:

  • Acquire All Scenes before Analysis: Acquires all scenes before the analysis is executed.
  • Acquire and Process Scenes Sequentially: Acquires and processes each scene sequentially.
  • Acquire and Process Wells Sequentially: Acquires and processes each well sequentially.

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Objective

Selects the appropriate objective for the overview scan (typically with a low magnification). If the objective has already been defined in the experiment, it is read only (greyed out) here.

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Optovar

Only visible if an optovar is available.

Selects the optovar for after magnification of the overview scan. If the optovar has already been defined in the experiment, it is read only/greyed out here.

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Find Surface before Overview Experiment

Only visible if Definite Focus is licensed.

Performs a Find Surface before the overview scan. This step is independent from and additional to any focusing strategy defined in the overview experiment.

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SW Autofocus before Overview Experiment

Performs a SW Autofocus before the overview scan and sets the found z-position as z-position for the overview scan. This step is independent from and additional to any focusing strategy defined in the overview experiment.

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Initial Range

Only available if SW Autofocus is activated.

Sets the range for the software autofocus.

Processing

Displays a section for processing steps to process the overview image before it is analyzed.

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Add Processing Method

Adds a step for a new processing method.

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Method

Selects a processing method from a drop-down list.
Available processing methods:

  • Airyscan Processing
  • Apotome Raw Convert
  • Deconvolution (defaults)
  • Shading Correction
  • Extended Depth of Focus

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Setting

Selects the setting for the processing method from the drop-down list.
Note: If you want to use Shading Correction with a reference image, you have to define your setting in Batch mode!

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Remove

Removes this entire processing step.

Image Analysis

Defines the image analysis parameters for the workflow.

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Setting

Selects the image analysis setting used to analyze the overview scan.

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Class

Only visible if you have selected an analysis setting where more than one class is defined.
Selects the class of the image analysis whose regions are used to perform the detailed scans.

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Add Stop Criterion for Detailed Scans

Activated: Displays options to define a stop criterion for the detailed experiment.

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Select Feature

Only visible if Add Stop Criterion for Detailed Scans is activated.
Selects the measurement feature that is used to sort the objects detected by the image analysis from the list of suitable measurement features defined in the image analysis.

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Select Order

Only visible if Add Stop Criterion for Detailed Scans is activated.
Selects the order for sorting the results.

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Random Selection

Only visible if Add Stop Criterion for Detailed Scans is activated.
Activated: Selects the objects randomly. Select Feature and Select Order are disabled.

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Max. Objects

Only visible if Add Stop Criterion for Detailed Scans is activated.
Sets the maximum number of objects that get scanned by the detailed experiment.

Repeat Detailed Scan

Activated: Displays parameters to repeat the detailed scan over time.

Cycles

Only visible if Repeat Detailed Scan is activated.
Defines the number of repetition cycles for the detailed scan with the slider or input field.

Interval

Only visible if Repeat Detailed Scan is activated.
Defines the minimum requested time between cycles with the slider or input field. The dropdown selects the time unit (minutes, hours, days).

Detailed Experiment

Defines the settings for the detailed scan.

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Experiment

Selects the experiment setup to acquire a detailed scan at the position of each object detected by the image analysis.

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Objective

Selects the appropriate objective for the detailed scan (typically with high magnification). If the objective has already been defined in the experiment, it is read only/greyed out here.

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Optovar

Only visible if an optovar is available.

Selects the optovar for after magnification of the detailed scan. If the optovar has already been defined in the experiment, it is read only/greyed out here.

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Find Surface before First Detailed Experiment

Only visible if Definite Focus is licensed.

Performs a Find Surface before the first detailed scan. This step is independent from and additional to any focusing strategy defined in the detailed experiment.

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SW Autofocus before First Detailed Experiment

Performs a SW Autofocus before the first detailed scan and sets the found z-position as z-position for the detailed scan. This step is independent from and additional to any focusing strategy defined in the detailed experiment.
If the detailed experiment is not a tiles experiment, the focus strategy is automatically set to the “standard” behavior, i.e. the selected autofocus strategy will be performed on each tile of each detailed experiment or each time point for a time-series, respectively. If you want to use a different strategy, e.g. perform the selected autofocus strategy on each n-th tile of each detailed experiment, you have to activate the Tiles checkbox for the detailed experiment.
Then you can select the desired frequency of autofocus in the Focus Strategy tool under Stabilization Event Repetitions and Frequency when you switch to Expert mode.

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Initial Range

Only available if SW Autofocus is activated.

Sets the range for the software autofocus.

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Recall Focus before each Detailed Experiment

Only visible if Definite Focus is licensed and if Find Surface before First Detailed Experiment is activated.

Restores the saved focus position and applies it for each detailed experiment.

Output Folder

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Output Folder

Determines the folder where the analysis results are saved.
A subfolder is automatically be created for each run of a Guided Acquisition experiment.
Note: When a ZEN Connect project is open, the output folder cannot be set here, but is defined by the ZEN Connect project.
Note: When using Guided Acquisition with Direct Processing, make sure that the processing computer has access to this output folder!

Open Output Folder after Execution

Activated: Opens the output folder after Guided Acquisition is finished.

Start

Starts Guided Acquisition.
The Start button turns into a Stop button as long as Guided Acquisition is running. Click Stop to stop the running Guided Acquisition workflow.