Stitching Images

Image stitching lets you combine multiple image tiles to create a single high-resolution image that is beyond the normal aspect ratio and resolution of a microscope's field of view. For best results, the acquired image tiles should have overlaps with distinctive features that can be used as reference points for aligning tiles accurately.

If you are unfamiliar with image stitching, you can follow a step-by-step tutorial that explains the main features of the Dragonfly Image Stitcher (see Image Stitching Tutorial).

Image Stitching Challenges

Sometimes, aligning images based on their image content is not always easy or even possible. For example, when two overlapping regions have very little content it can be almost impossible to tell how they should be positioned. Or when the overlapping region depicts a structure like a straight line that is translationally invariant it may not be possible to automatically derive a precise position of the overlapping images. In such cases, you may need to work on sub-sections of the tiled image mosaic and then stitched the aligned sections together.

You should also note that poor image quality, such as low contrast or the presence of excessive noise, can adversely affect the performance of the automated alignment methods. For such cases, you may have to process your images accordingly before attempting any stitching operation (see Image Filtering). Pre-processing may also be required if the brightness and contrast of the unique image tiles varies within your dataset.

  1. Right-click the volumetric dataset with the images that you need to stitch in the Data Properties and Settings panel and then choose Image Stitcher in the pop-up menu.

    The Layout Editor appears in the Image Stitching context.

  2. Do one of the following:
    • Click the Grid Layout tab, if you need to choose how the image tiles are arranged for stitching.

      Select the grid that corresponds to the type of collection used to acquire the image data (see Choosing Image Grid Layouts).

    • Click the Configuration File Layout tab, if you need to load a configuration file that contains the coordinates of the image tiles within the selected dataset.

      Load the configuration file, as described in the topic Loading Configuration Files.

  3. Determine the best strategy for aligning the overlapping images.

    In cases with good image content it may be possible to stitch all the image tiles sequentially. In other cases it may be best to stitch images tiles pairwise.

    For complex cases with varying image content, it may be best to work on subsections of the data and then stitch the aligned groups together. You can move selected tiles with the Move tools (see Translating and Rotating Objects).

  4. Select an alignment method — Template Matching, Feature Base, or Value Stitcher — and the settings for the selected method (see Alignment Methods and Stitching Settings).
  5. Select the image tiles you want to align and an application, or stitching pattern, for the selected To Stitch image tiles. See Stitcher Panel and Settings for information and explanations about the different alignment methods and settings.
  6. Click the Stitch button to align and then stitch the selected image tiles.
  7. Evaluate the stitching result.

    If required, you can apply an additional automatic alignment or use the Value Stitcher and Move tools to refine a selection.

    If there are obvious seams between the aligned image tiles, you can blend the overlapping region so that the stitched result appears seamless (see Blend Options).

  8. Save the stitching result as follows:
    • Enter a new name for the stitching result, if required.
    • Choose Channel if you want to save the result as a new dataset.
    • Choose Configuration File if you want to save the result as a configuration file only.
  9. Click the Save button.

A number of configured actions and keyboard shortcuts are available for working with Dragonfly's Image Stitcher. The default settings for these actions are listed in the following table.

Default configured actions for the Image Stitcher

Action

State

Key

Mouse

Select channels (Reference)

stateRefSelectionOne_OrsDatasetStitching

 

Left mouse

Select multiple channels (Reference)

stateRefSelectionMultiple_OrsDatasetStitching

Left Ctrl

Left mouse

Switch to multiple reference selection mode

 stateRefSelectionOne_OrsDatasetStitching

Left Ctrl

 

Switch to reference selection mode

 

 

 

Select channels (To Stitch)

stateToRegSelectionOne_ORSDatasetStitching

 

Left mouse

Select multiple channels (To Stitch)

stateToRegSelectionMultiple_OrsDatasetStitching

Left Ctrl

Left mouse

Switch to multiple To Stitch selection mode

 stateToRegSelectionOne_ORSDatasetStitching

Left Ctrl

 

Switch to To Stitch selection mode

      

Display next slice (in Image Stitcher)

 

Left Ctrl

Mouse wheel up

Display previous slice (in Image Stitcher)

 

Left Ctrl

Mouse wheel down