iannellog
commented
6 years ago TeraStitcher proved to be quite robust in these years, and the problem you mention has not a clear reason. It is likely there is something wrong in the way you have used the tool, but of course this is not immediate to find. Could you please answer a few question just to clarify some point and exclude some possible problems?
- is the first time you use TeraStitcher or you have already used it successfully?
- are you using the command line version or the GUI version?
- are all tiles complete (all have exactly 2007 slices)?
- the xml file you sent to me has been generated by some script developed from you (probably yes, but I want to be sure)?
- one weird thing is that you use real numbers to give a value to attribute ABS_V and ABS_H in tag Stack; the tool actually expects an integer and I do not know which kind of conversion is carried out; it should not be this the problem, but it is better to use integers (in any case the tool is not able to provide a sub-voxel precision)
- another thing to be clarified is if you have run the align step: the xml you sent me is the import xml file, not the file generated after the correct alignments have been computed; have you used this file to generate the image you sento to me?
- to which slice corresponds the image you sent me? is it the test slice generated when you import the dataset? It is likely I will have to ask you more things, but we can begin with these. Best.
-- Giulio
2018-07-06 19:04 GMT+02:00 Lalga notifications@github.com:
Hey, So I tried using Terastitcher to stitch some image tiles I obtained, and the end result ending up looking like below. For the most part, the stitching worked well and the tiles were merged correctly, but there are some obvious errors as well. There are many sharp edges at the ends of tiles, suggesting that this tile likely isn't supposed to belong in that spot. This is most evident near the top of the image, and near the right side, where a vessel seems to be cut off abruptly. In addition, there is the large black space near the right and bottom edges of the image, where data should be. The raw data is definitely not blank, as I've done the same stitching with ImageJ and didn't run into this issue. Either way, any idea how to fix this? I've attached the xml file below.
[image: capture] https://user-images.githubusercontent.com/33734415/42391052-feaadbee-811b-11e8-8bc4-cbb783edb2a3.PNG Mouse hemisphere parameters.txt https://github.com/abria/TeraStitcher/files/2171365/Mouse.hemisphere.parameters.txt
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--
Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy
Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ
Lalga
Hey, So I tried using Terastitcher to stitch some image tiles I obtained, and the end result ending up looking like below. For the most part, the stitching worked well and the tiles were merged correctly, but there are some obvious errors as well. There are many sharp edges at the ends of tiles, suggesting that this tile likely isn't supposed to belong in that spot. This is most evident near the top of the image, and near the right side, where a vessel seems to be cut off abruptly. In addition, there is the large black space near the right and bottom edges of the image, where data should be. The raw data is definitely not blank, as I've done the same stitching with ImageJ and didn't run into this issue. Either way, any idea how to fix this? I've attached the xml file below.