Hi all. Have anyone figured out an easy way to stitch images acquired using stack and scan feature? Thanks

Thanks William. I saw those posts before. I was able to stitch using ImageJ using a simple script that I made. However, the biggest problem I have is that the file names generated by open flexure software are confusing. It saves the images as using the X, Y, Z coordinates I think. It will be much ea…

Hi I’ve been looking at ways to stitch images and I’ve found (but not tried for now) these: https://pages.nist.gov/MIST/ https://www.microsoft.com/en-us/research/product/computational-photography-applications/image-composite-editor/ -> this is not open source and there are a few tutorials on you…

I just started using Microsoft’s Image Composite Editor like you described above. The part for me that was hard to understand was setting up the Stack and Scan and what direction it would go? How many steps to configure it for overlap of the images at say a 50% overlap? I find that “Snake” makes the…

That is a good stitch on a very challenging image. There is a lot if blank area that does not give the algorithm very much to go on to match up where it should be joined together. Something with detail all across the slide will work much better.

I tried to run the stitching again with steps at 2500 to get more overlap. To scan the whole stage requires 20x20 steps then, so 400 images instead of 100 images, which takes MUCH longer to run. [image] Whew! That took 2776 seconds or 46 minutes. It was about 106MB for the images. [image] I tr…

Hello! If you want to upload your images for me to download somewhere I can give it a go using my method and report back to you. Then if it’s successful I can detail the steps for you. I’ve found ImageJs stitching tools to be much better once you get the parameters right. N.B - to combat your prob…

Thanks so much nonacastro for the links. I was not aware of the MIST software. I will try it and report back. Gracias por tu ayuda!

Thanks John! I really appreciate you took the time to comment on my post. I went through the same hoops and loops to get a stitched image. However, I used ImageJ which gave me better results and can support stacked images as well. Like William said, I found that large blank areas are not ideal for …

I agree on ImageJ. I use it a lot and get good results. As you can see in my post above, is hard to sort by date because many images have the same timestamp.

Stitching images

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WilliamW 25 September 2020 21:10 2

I don’t think there is a native openflexure stitcher. A couple of mentions of successful stitching on the forum here and here .

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Stitching images

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