Atlas Question
Added by Anonymous almost 15 years ago
When I stitched together an Atlas on the TF20 the other day, I noticed that the jump between the different exposures where fairly big. The resulting Atlas appeared to be mostly complete, but the squares did not quite match up at the boundaries (that is, squares on the grid that got cut in half at the image border were not aligned properly). Is there any way I can improve the stitching quality of the Atlas process? How important is it for leginon that the squares look like squares?
I didn't really have this problem with the T12--my guess is that it ended up taking shorter step sizes and the additional overlap allowed Leginon to make a more accurate stitching due the higher number of correlations (?).
Thanks for the help!
Replies (2)
Re: Atlas Question - Added by Jim Pulokas almost 15 years ago
Leginon does not use any correlation technique to stitch together the images. The positioning of image tiles within the final atlas is accomplished using only the stage position calibration. The best way to improve the quality of the atlas is to do a better stage matrix calibration.
However, the other question is: How important is it to have a good quality stitching? It may not matter. The best way to find out is to make an atlas, then pick a target at one of these squares on the border of two tiles. Since the two tiles do not stitch together properly, you have to estimate the best place to click your target. You could trust one or the other tile as to where the center of the square is, or you can take an average center based on both of them. When the Square node acquires the final image of the square, you may find that the squares are not centered properly. This could be because the stage calibration was bad and it could not move to the target. It could also be because your grid preset and square preset were not aligned to each other before you acquired the atlas. In other words, you move to a square properly, but when it switches to the square preset, the square is not centered anymore.
In any case, you can try to improve your calibrations and preset alignments, but you have to decide if it is worth your time to make everything perfect. Don't forget that your ultimate goal is to get good high magnification images, not well centered squares and good looking atlases. Therefore, high magnification targeting (from hole to final exposure) is the most important. Low mag calibrations can be a little sloppy if you can tolerate it, and it does not cause frustration and confusion during the data collection process.
Re: Atlas Question - Added by Anonymous almost 15 years ago
Thank you! I found out yesterday that you were right--it doesn't really matter. Some of the targets I picked were at the boundary of the stitching, but it was able to find the square relatively well.
Thank you for clearing that up!