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Reduced intensity at tile boundaries #2
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Hi, Unfortunately the boundary effect, which we call "zebrated pattern", is a common issue for different microscopy techniques and our SPIM images too have the same problem. We implemented a very simple method (still experimental) to correct this: see the This method extracts the illumination map during the Align step and then corrects the tiles using the computed map during the Merge step. More sophisticated methods have been proposed in the literature, but so far we did not spend too much time on this because it does not seem to be an obstacle for effective image analysis. If this method fails, you might want to better characterise the problem on your images and implement a custom correction method. In this case, you can disable blending between adjacent tiles (automatically done by TeraStitcher) by providing Hope that helps! Cheers, |
Hi Alessandro, |
Hi Alessandro, I am facing a problem with stitching process when I am trying to use a down sized volume. |
Vivek, the problem is due to the relatively small number of slices along Z and occurs in the Align step https://github.com/abria/TeraStitcher/wiki/Step-2:-Align. To estimate misalignments, TeraStitcher looks in a search region whose radius along Y, X and Z axes is specified with --sV, --sH, and --sD command line parameters, respectively. Their default value is 25, which means that the search region will have size 50x50x50 by default. That’s too much since you only have 50 slices. On the Vaa3D-TeraFly, the default value is 20, which is still fine in your case (but would produce an error with 40 or fewer slices). Then the solution is to provide --sD=20 (link https://github.com/abria/TeraStitcher/wiki/User-Interface#--sdinteger-advanced to parameter description) on your command line during the Align step. My warning is that if your maximum “expected” misalignment along Z for a pair of adjacent stacks is too close to the number of slices, the stitching result might not be good. In general, it could also be possible that the problem has no solution. That’s because to find a misalignment between two images, there should be some overlap. The smaller the overlap, the more difficult is to find the misalignment. No overlap, no solution. Hope I helped :-). Cheers,
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Hi Alessandro, Thanks a lot for your another quick response. I highly appreciate. Thanks On Wednesday, November 11, 2015, Alessandro Bria notifications@github.com
Vivek Kumar |
Hey Alessandro, Sorry, I have another question to disturb you. Thanks |
Hi Vivek, unfortunately I did not completely understand your problem. What is “exec_sti.exe”? TeraStitcher does not create such a file :-). Anyway, TeraStitcher is currently not able to generate multichannel images (but can read them). We already developed the underlying code, and we will release this feature soon (1-2 months). Meanwhile, here is a workaround:
TeraConverter (GUI version) is available in Vaa3D (Menu Advanced > Big-Image-Data > TeraConverter). You can download Vaa3D from www.vaa3d.org http://www.vaa3d.org/. Let me know if you need further assistance. Best,
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One more comment: steps 1-5 should be run once on the "best" channel (i.e. the one providing most of the information), whereas step 6 should be repeated for all the channels taking in input the same .xml file previously generated at step 5. |
Hi Alessandro, Thanks a lot for your great help.
Vivek Kumar |
Hi Alessandro, |
Vivek, you don't need to edit the xml_merging.xml file to start a new step 6. Just use the same file and start a new step 6. To select the channel to stitch, use the --imin_channel parameter as indicated in my previous post. Cheers,
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Hi Alessandro, Problem its flipping the tiles in vertical axis. So if look at the image, each tile appears to be vertically flipped 180. Horizontal position of tiles look normal. Please if you can take a look at this. Thanks a lot. |
Sorry I forgot to mention that it could also be shifting the whole column of tiles from left to right side and vice versa. I wonder if I have made my point clear. Thanks |
As to the flipping problem, you have to specify correctly command line options --ref1, --ref2, --ref3 in the import step. Have a look to the attached file for details. If something is not clear please write again because we are trying to improve the documentation about these issues. One more observation about the values of command line options --sV, --sH, --sD when pixel size is 0.234 in x-y. Best. -- Giulio |
Hi Alessandro,
First, I must say this is a great work from you guys, thanks.
I recently started using Terastitcher for large image sets.
If you look at the image below (cropped image), you can see the boundary effect between tiles, i.e. intensity is relatively lower at the stitched junctions. I have seen this before also in some articles.
What could be the possible reasons and solutions (e.g., percentage of overlap can be tweaked to reduce this, etc.). I have tried normalization on these images but the difference way significant a the boundary.
Thanks
VK
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