Stitching Images from Your Manual Microscope
Introduction
Tiling microscope images allows one to stitch together a larger montage image with the resolution of the individual tile images. Traditionally this has been done with an automated XY stage to acquire the tile images. In this note we report making large field of view (FOV) montage images from manually positioned and acquired tile images using a simple freeware software originally made for panoramic photo stitching. This software, Autostitch, does not require the use of file name parsing to identify tile location. As long as a contiguous object spans two or more tiles, the software locates them automatically.
Method
To use Autostitch, go to https://autostitch.en.softonic.com/ and click the Download button shown by the red arrow.
Find the zipped file in your Downloads folder, unzip the file and create a shortcut on your desktop.
When taking images it is recommended to have 10-20% overlap between images. It’s best to keep your eye on a location near one edge of the image and move the sample such that it remains in the FOV but at the other side of the image. Make sure all of the images are saved in the same location for easy access. One of the advantages of Autostitch is that it does not use the file name to decide where the tile is located and as a result no special file formats or naming conventions are required.
To use Autostitch, click the Folder icon in the application. Direct the application to the images to be stitched, select them all, and click OK. A montage image will be produced and saved to the desktop with the name “pano.jpg”. Subsequent stitching appends a numeral to the file name (pano1, pano2, etc.).
Clicking the Settings icon in the application allows one to adjust parameters like output image size and jpeg quality. It should be noted that most image formats can be stitched but the output will be jpeg.
Setting the JPEG quality to 99 will maximize the resulting montage. Tile images with no objects in them or with no overlap may fail to be incorporated into the montage and can result in some over fitting distortion.
Results
Generating large FOV montage images can be created by manually acquiring adjacent but overlapping images. Autostitch allows the assembly of these images into a montage image without critical alignment or naming conventions. The resulting images are produced in the JPEG format and can be cropped to remove unwanted regions in any photo editor. This freeware utility is very helpful for assembling manually created tiled images.
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6 年Just a short comment from a Zeiss support guy: We offer the ?Panorama“Function in both Axiovidion and the actual software ZEN blue, even in basic functionality with camera on manual microscopes. One important limitation is in confocal this in confocal imaging where are forced to get a motorised stage. If a software like imageJ or even commercial companies support this you can even get this.. The moment you need to understand 3D-relationships or even 4D-imaging I would clearly advice to go for motorised XY-Z Imaging. Additional multi-modal analyses can be Adressen by 3rd Party Software like share w?re (imageJ/fiji including online feedback loops in ZEN)!as well as as professional Imaging software like Imaris, Amira, Arivis etc. Which one can use in combination with feedback loops using Python. Scripting in ZEN blue. So if you APPLY for money include these ideas in your planning! If you are limited in your budget: Talk to your sales rep: There ist a variety of options to go for depending on you installed hardware and software base!
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6 年Coleman Murray