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abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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Aligning step - OK to close and restart TeraStitcher? #8

Open JimboMahoney opened 7 years ago

JimboMahoney commented 7 years ago

Hi Alessandro,

Is it OK to run the Aligning step so that the alignment xml files are created, then restart TeraStitcher and run the Merging step?

I'm assuming that TeraStitcher looks for the alignment files and if it doesn't find them, it falls back to stage coordinates as the tooltip suggests.

The reason I ask is that I am stitching 2D tiles and don't notice any difference in the image when aligned in this way or not.

Therefore, I'm not sure if either or both of the following are true:

1) Aligning with 2D images in TeraStitcher is pointless and has no effect. 2) Closing TeraStitcher after the Aligning step and then starting it again to run the Merging step ignores the alignment files.

JimboMahoney commented 7 years ago

Played some more and it looks like it's option #2 - TeraStitcher seems to ignore the files if closed and then open again.

abria commented 7 years ago

I confirm (1), it is a bug of 1.9.62 (only for 2D stitching). We are currently working to fix it.

As to (2), the Align step generates an xml file xml_merging.xml in your image folder. If you close and relaunch TeraStitcher, you should explicitly load this file with Open XML... button in order to resume your stitching process from the point you interrupted. Otherwise TeraStitcher will start a new process and reload the stage coordinates.

JimboMahoney commented 7 years ago

Hi Alessandro,

I'm getting a problem with the search region, which if I'm reading it correctly, should actually be OK:

image

image

I think the overlap here is greater than 2*overlap+1, right?

abria commented 7 years ago

The search region should be chosen within half of the overlapping extent, for each direction. What is your overlap (it is displayed in the advanced options) ?

JimboMahoney commented 7 years ago

Hi Alessandro,

Can see the overlap in the screenshot? The search region is 20 voxels and the overlap is 148 (Y) and 175 (X).

abria commented 7 years ago

Sorry, I missed the second part of your post. Yes, the settings are OK, but as I said there is a bug in the Align step for 2D images. Actually your image is 3D (you have three slices), but still too thin for the 3D stitching to work properly. We are working on this and will let you know when it's fixed.

abria commented 7 years ago

BTW you can try to reduce the search region along Z from 20 to 1. But still it won't generate the correct stitching due to the aforementioned bug.