Large-image Acquisition

(requires: Stage XY axis)

A motorized XY stage is required to have the Large Image tab enabled within the ND Acquisition window. When set to work, it captures several frames within a defined area and stitches them together, so you get an extra large image.

Note

When camera ROI on Live Image is on (see: Camera ROI), only its frame defining the sensor area is used during the scanning.

Special Options

Distortion Correction.ai

(requires: Local Option)

This function attempts to correct for geometrical image distortion, which is an unwanted effect of certain optical systems and manifests itself as duplicated sample structures near the overlap regions of large image tiles.

Some hardware configurations are more susceptible to this effect than others, but the most common source of the problem is a camera coupled with a relay lens with a zoom other than 1x.

This is an example taken by a Nikon Ri2 camera with a 1.8x relay lens:

The green crosses mark the boundaries between large image tiles.

The correction proceeds in two steps:

  1. Calibration for the current hardware configuration.

  2. Application during large images stitching.

Start the calibration by clicking the right mouse button inside the Live image and selecting Create Distortion Correction Maps for Current Settings.

The function is designed to work for both bright field and fluorescence modalities. Before running this function, make sure you see a focused, sufficiently bright but not oversaturated, dense sample that ideally covers the entire camera field.

Note

Samples with periodically repeating structures (e.g. calibration slides), samples not covering the FOV or samples not in focus are not suitable for calibration.

Examples of suitable and unsuitable scenes:

After the calibration is successfully finished, the computed distortion maps are saved to the NIS-Elements platform folder and tied to the current hardware configuration (microscope port, objective, camera ROI, light wavelength, zoom, etc.). You can run the calibration multiple times for different configurations.

The application of the distortion maps can be switched on in the Acquire > Scan Large Image function. Make sure you use identical hardware settings as in one of the calibration runs, otherwise the correction will not be applied.

Scan Area

The area can be defined in three ways:

Define by setting an array of frames

Check the first radio button and define the number of rows and columns of the scanning grid.

Set the Area Size

Check the second radio button and define the size of the scanned area in millimeters.

Pattern

Click the Browse button and select an XML file containing a large-image pattern.

This XML can be created using the _LargeImageGrabbingFreeShape macro function.

Caution

Do not mistake this XML with similar XMLs created by other functions. For example, XML files saved via the Acquire > Capture Multipoint > Capture Automatically window will not work here.

Stitching

Define the stitching method:

Overlap

Enter the percentage of image overlapping which is used for image stitching.

Image Registration

If checked, the system automatically stitches the images together to form a large image using a precise stitching algorithm (image registration). If there are more channels available, select which one to use from the pull-down menu (Use).

If unchecked, the system will stitch the images together with the defined overlap using the recorded XY coordinates but without using the Image Registration algorithm. Stitching can also be done manually after the acquisition finishes via the File > Stitch Large Image from Files command.

Close Active Shutter during Stage Movement

See Common ND Experiment Options.

Use PFS

If checked, the Perfect Focus System (PFS) is utilized. A new PFS column is shown in the table with a <- button filling in the PFS value. Context menu over the value enables the user to Offset All Points in PFS or to Reset All PFS Offsets which sets the same (current) offset for all points.

Use Focus Surface

Focuses using the surface defined in the Focus Surface tab of the View > Acquisition Controls > XYZ Overview panel.

Advanced Settings

Execute Command before Capture, Execute Command after Capture

See Executing macro commands during ND acquisition.

Wait before each capture

This delay between captures can be used for sample stabilization, e.g. after XY movement or autofocus.

Commands for large image acquisition

NIS-Elements offers multiple ways how to capture a large image:

Acquire > Scan Large Image

The most complex large image acquisition.

Acquire > Manual Large Image

Custom large image acquisition for manual area selection.

About ND Acquisition

A tab inside the ND Acquisition window used when the area of interest exceeds the camera FOV.

_LargeImageGrabbingFreeShape

A large image created by stitching (obsolete function only executable by a macro).

_LargeImageGrabbing

Large image grabbing (obsolete function only executable by a macro).