FEATURE REQUEST: Ignore Zeros and Specify Peak for Grid/Collection Stitcher

[iomega15]

There are two very useful options in the Pairwise Stitcher that are absent from the Grid/Collection Stitcher:

1. "Ignore zero values when fusing", and 2) "Check Peaks" slidebar.

I care more about the first one, because for Selective Plane Illumination Microscopy (SPIM) the data is has a parallelepiped shape. So we are unable to use the Grid/Collection Stitcher, because it doesn't have the option to ignore zeros. Thanks.

[imagejan]

@iomega15 did you consider using BigStitcher? It has many more options to tweak your stitching, I don't know however if suits your case...

[iomega15]

@imagejan , we tried out the BigStitcher. It does have the capability we need. However, it does not produce the TileConfiguration.txt with coordinates. We did find the affine transform matrix buried within the xml, but I wish there was more documentation about it. It took us some time to figure out that even though the 3d affine matrix should have a size of 4x4, you are actually skipping its degenerate row (or column, depending on the convention), so your matrix has 12 elements instead of 16. This matlab link was very helpful: https://www.mathworks.com/help/images/matrix-representation-of-geometric-transformations.html#bvnhvau
Also, it would be helpful to know which other programs are able to read the xml language. For example, we tried this one, but it failed: https://www.visitusers.org/index.php?title=Using_XDMF_to_read_HDF5

[iomega15]

@imagejan , I don't see an "Ignore Zeros" option in the BigStitcher. Does it have it?

[StephanPreibisch]

Hi, we will provide a small hack to export and import something like the TileConfiguration in the BigStitcher, it is already on our list @hoerldavid