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Software / Translation Tools

Image Stitching Tool

Microscopy Image Stitching/Montaging Tool for Windows

Stitch/combine stacks or individual images with the translation tool software suite from Indigo Scientific. Designed for HREM images but can be used with all types of grey scale images. Montage monochrome microscope images via drag and drop tools.​

Stitched Microscope Image of HREM sample Mouse Showing High-Resolution Stitched Images

Overview

We have 5 main tools in the Translation Tool application that aid in stitching images or combining mis-aligned stacks.

  • Row Column Stitcher – Stitches images using user defined X and Y locations for both a row and column.

  • Map Stitcher – User places images into a blank canvas to align images.

  • Fixed XY Stitcher - Tell the software the pixel shift between images and it calculates the whole map.

  • Auto Stitcher – An algorithm deduces X and Y locations of images and places them.

  • Z Alignment – Aligns two stacks using manual X/Y positioning.

Row Column Stitching

Stitching tool HREM

Row/Column stitching mode is an easy way to combine automated positions captured from an XY. Where each row and column is perfectly spaced. The stitcher will ask you to manually place the rows and columns and manually you combine the images.

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This can mean you can create accurate large stitches with not much in the way of PC resources. The picture above shows a 2x2 stack stitched from a HREM image.

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The images are blended to create a perfect blend of focus and illumination between images. When the translation is found it can then be applied to a stack or other images.

Map Stitching

Stitched microscope image example showing blending

Combine images together completely manually with no blending with the map mode, this allows you to combine any image together on one big map. This mode does not blend images, but can be used for non patterns.

Auto Stitching

A feature finder is used to combine images, although this takes out the user computation it can mean higher resources required and can take a while or end in failure. But for smaller scans is a simple way to create stitches.

Fixed XY Stitcher

Place values in the X/Y and images per row and generate whole stitches from just these values. Store them for later use with the same objective.

Deciding on a Method

  • For a use case of a 10x10 scan we recommend using the Row-Column Custom Stitcher this is because it will create the resultant image easily with little computation especially for a large dataset. It will also not crop the images for blending so you will not need to worry about alignment.​

  • If you have no overlap or random image placement in the stack, the Custom Map Stitcher is ideal, it is a blank canvas to align images and expects no images. Put images in any order or location you like on the blank canvas.​

  • If your images are almost perfectly aligned to the XY platform (camera is aligned to the XY stage), and you have a small stack (2x2), the Auto Stitcher is ideal. It will create accurate images but may struggle on larger datasets with no data.

  • If you know the X/Y differences the fixed position stitcher is the best option.

Title
> 3 x 3 (Ultra Resolution Scan)
< 3 x 3
<0%- 5% Overlap
Severe XY Drift (Camera Alignment)
Aligning Two Image Stacks
Stitching Random Microscope Image
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Image Stack Alignment

Sometimes with image stacks Z alignment of two individual stacks is necessary, such as an issue with alignment. This tool takes two images and moves the images at the point where you request to make them fit manually. 

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This alignment can then be applied to the whole stack.

Z Alignment Software Example

Image Stack Interpolation - Single Image

Interpolated volume stack image replaced section from mouse embryo stack

In serial imaging we expect perfect images all down the stack, sometimes there may be anomalies in a stack through the environment such as resin becoming stuck to the surface of a block, lights being switched off etc. So we have a tool for interpolating two images on a Z stack, not a replacement for the real data but will allow a stack to appear seamless without missing sections.

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How it works:

  • Whole image stack is acquired (stitched if necessary)

  • Locate the troubled section

  • Select the images either side of this image and click go

Contact our Image Stitching Experts

Have a feature request or need help? Contact our friendly team for more information.

Phone:
+44(0) 1462633500

Email:
hello@indigo-scientific.co.uk

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