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Z Scan

Z Scan is a linear spatial scan using a single axis motor drive. The Z Scan allows images to be captured for display, archiving or processing, while incrementing a Z axis position of the motorized focus controller device for each image. This can provide the ability to collect spatial information on static objects outside of a single field of view. To setup a Z scan go to the Sequence pane and select Z Scan from the Select Scan Type drop-menu. Once the scan has been setup use the Save Scan icon to save scan settings for repeated use. Use the Open icon to load a saved scan.

Progress

• Event Markers - Can be added to the data document file during acquisition as notable events occur in the experiment. Both the numbered buttons above and keyboard numbers may be used.
• Time Elapsed - The time from the start of the first scan.
• Delay Remaining - A reference to delay time. The right arrow button may be clicked to exit the delay.
• Frame Count - Total number of frames captured.
• FPS - Frames per second captured

Scan Settings

The Scan Settings panel is easy-to-use, simply set the speed, define the capture interval, enter the number of passes to capture and where to save the data.

Storage and Display

Use AutoSave to define where and how to store acquired data.

• CXD: Image data is organized and saved as a data document
• TIFF: Captured data is saved as individual image files
• MPTIFF: Captured data is saved as multipage tiffs

Determines how the data is structured when written to a data document.

• To a Single File: Store captured image data in successive fields.
• One File Per Pass: Store captured image data for each pass in a series of data documents called a Summary DocumentA Summary document (.cxs) is a collection of data documents (.cxd)..
• One File Per Position: Store captured image data on a positional basis. A Summary document (.cxs) is created with a Data Document (.cxd) for each position.

Determines if a live view is displayed in the image display or if acquired images may be reviewed during the acquisition.

• Update Image Display: During a sequence captured images are displayed in the image display
• Review Images: During a sequence captured images may be reviewed as newly captured images are added.

Speed

Select the maximum speed or a type of delay.

• Enable Maximum: Capture to memory at maximum speed. During maximum speed, items which slow down acquisition will be ignored (i.e., exposure protection and Z auto-focus).

• Field Delay: A pause between each frame of the scan. Enter a numerical value followed by units. (e.g., 5 seconds = 5s)

• Pass Delay: A pause between subsequent passes in a multi-pass scan. Enter a numerical value followed by units. (e.g., 2 milliseconds = 2m)
• Hours = h
• Minutes = t
• Seconds = s
• Milliseconds = m
• Microseconds = u

• Disk: Stream data directly to disk
• Memory: High speed acquisition stream to memory
• RAM: Sets the limits for the amount of RAM available for streaming

Control

Defines a specific Frame, Pass or Time point to stop the current scan.

• Continuous: The scan runs according settings without a preset endpoint. The scan will be stopped when resources run out or can be interrupted using the Finish button.
• Pass Count: Defines a specific number of passes to complete the current scan.

Z Scan Setup

The Z Scan Setup provides multiple options for setting up a Z scan. If the system is setup with two Z motors use the Active Z drop-menu to select the desired device. The Lambda Z option is available for capturing up to 5 mono channels. The Lambda Z works by acquiring separate Z scans for each channel; i.e., channel 1 Z scan, channel 2 Z scan, repeat up to 5 channels.

Manual Focus Controls

Manual Focus Control is available using software or by using the manual override controls e.g., joystick or focus controller knob, to allow positioning of the Z axis. Focus devices are installed in the Device Setup Menu of the Current Profile.

Z Position Slider

The Z Position Slider allows the Z position to be changed by clicking and dragging the slider handle. The movement of the slider is relative, not absolute, so dragging the slider further up or down the scale will produce a faster movement in that direction. Note that it is possible to focus up and down, faster and slower without releasing the slider.

Top Focus Limit

The Top Limit can be set to prevent the Focus position from being incremented past a certain value. This is not the case when using the manual Joystick control that will override the limit and force the limit to a new position. Checking the Top limit will assign the current position to the limit, or the position can be numerically entered. Clicking the Top button will move the Z axis to the top position. The Top Focus Limit is also used when computing a Z-Axis Scan.

Caution: Be very careful when using the Top and Bottom buttons! Make sure that the Top and Bottom focus limits are within an acceptable range. Improper setup could cause serious damage to the sample, microscope objectives and/or other equipment.

Current Position

The Current Position is constantly read from the controller and displays the current location of the Z-Axis. This number can also be input numerically to instruct the controller to drive to a specific position.

Zero Position

The Zero Position button provides a choice of two functions:

1. Move to the existing Zero coordinate.
2. Set the current coordinate to be the Zero position.

Bottom Focus Limit

The Bottom Limit can be set to prevent the Focus position from being incremented past a certain value. This is not the case when using the manual Joystick control that will override the limit and force the limit to a new position. Checking the Bottom limit will assign the current position to the limit, or the position can be numerically entered. Clicking the Bottom button will move the Z axis to the bottom position. The Bottom Focus Limit is also used when computing a Z Axis Scan.

Increment

The number of steps to move between captures.

Count

The number of steps based on the size of increment in the Z scan.

Note: Use "Increment" in conjunction with the "Count" to acquire an appropriate number of sections based on the thickness of the sample and the resolution of the optics. For example, a typical 1.4 NA 63x Oil immersion objective should sample at approximately 0.45 micrometers to satisfy the Nyquist theorem. Adjust the range such that the reported range is equal to or larger than the objects which are being sampled.