-
Notifications
You must be signed in to change notification settings - Fork 2
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Are these stitching results correct? #28
Comments
Hello, My initial reaction to this is that the montage may be under-regularized and optimizing by producing a sheared representation of the tiles. As the optimal regularization parameter lambda is dependent on a number of factors (principally the number and weight of point correspondences), you likely need to change this. One sanity check on what a minimally deformed montage should ideally look like is to solve for a TranslationModel, which should produce a translation-only montage that looks like optimal stage coordinates. This translation model is what the solve is regularized against using the "translation_factor" variable (which describes the relation of the translation to the higher order transformation in the solve), so tweaking the value of that or lambda will vary how deformed your montage can be in service of bringing correspondences closer together. In the elife paper we described a method of exploring the tradeoff of some of these parameters. I am not sure if this figure made it in (was originally supposed to be a supplement), but it describes some of the effects of regularization on the section rendering. note that the "individual tile" part of this is actually describing the corner overlap of multiple tiles, hence why you see a seam. I have raised AllenInstitute/asap-modules#250 describing the addition of automated parameter search to the main repos. If you believe this is a rendering error, however, it would be good to understand why -- can you share some example tilespecs (in json form) so it's possible to visualize the stitching result? Thanks, |
Hi @RussTorres I will change the following parameters in The tilespecs produced by me can be downloaded from https://drive.google.com/file/d/1L7sROWEliXa5nLOPj7KerjBA2zjFLSS-/view?usp=share_link Thank you to further provide the file regarding the automated parameter searching. I am looking forward to seeing that. Thank you. Best and sincere wishes, |
Hi RussTorres, After change the
I attain resonable 2D stitching results with images from The tiles I used indeed have about 50% overlappings as indicated by the red and green lines: In each section, there are 9 tiles as shown up. Besides, the other parameters used in Hi RussTorres, could you help me stitch the above 9 tiles? You can easily download them from https://drive.google.com/drive/folders/19Wg4sVyw3v9-2z_b9LjCbzjVOTvAjdj-?usp=share_link Thank for your help, Dr. RussTorres. Thanks, |
Hi Dr. Russ Torres, The key changes I did were increasing the values of |
Hi Russel Torres,
The following image is a 2D stitching result following the
asap-modules
https://asap-modules.readthedocs.io/en/latest/index.html.The metadata I test is
21617_R1_166_T5_15_20201231140731_20201231140731
provided by you. Followings are visualization error maps with a html format:Are these stitching results correct? Why do they look like undergoing a spatial rotation? In addition, I also test some EM tiles sampled by ourselves, the 2D stitching results are also rotated by some degree. How do I solve the above problem?
Thanks in advance, Russel Torres. Thank you!
Best and sincere wishes,
MY
The text was updated successfully, but these errors were encountered: