PiAutoStage - Stitching

Stitching

Combining Individual images into a Mosaic

To create the highest resolution images possible, the PiAutoStage utilizes the high-quality optics of an existing microscope. The trade off is that it is not possible to image the entire sample in one frame. This requires the PiAutoStage to take many pictures (hundreds to thousands of frames) that must then be combined into an image mosaic.

Image Mosaics

The construction of mosaics from PiAutoStage images can be straightforward. The Python script addresses the mosaic structure (combing motion) for the frames. The user must tailor the image overlaps (40-50% overlap is ideal) required for alignment of the frames. Existing software can process the collected images into an image mosaic.

Stitching Software

-Image Composite Editor

-Image J/Fiji

Animation. Three blue rectangles appear in a row. Three orange recangles appear next to the blue ones. All rectangles change color to become one green rectangle.

Stitching of individual images into a mosaic.

Common Problems with Stitching

Poor Image Alignment

Usually caused by either: (1) loose components within the PiAutoStage or (2) a thin section that is too small for the sample carriage and moves around within the carriage.

Insufficient or Excessive Overlap Between Images

Overlap issues can be fixed by modifying the number of steps in the offending direction. Too little image overlap can be fixed by adding steps while excessive overlap requires reducing the number of steps.

Three blue recangles appear in a line. An orange dashed line appears in the center of the line. Three new recangles appear but are not in a line. Orange line appears on the second set of rectanlges to show they are out of alingment.

poor image alignment: Usually caused by loose components in the PiAutoStage.

Three sets of three recangles appear. The first set overlaps the correct amount, 40-50%. The second set overlaps too little. The third set overlaps too much.

Overlap Problems

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