Bigstream deformable registration

[neugun]

Hi Greg,

I have successfully run your big stream registration in the pipeline. It works well, and most of the cells can found their correspondence in the moving rounds. It is awesome!

Although Bigstream works well with the cell-level resolution, recently, I am wondering can we apply it to the single-molecule resolution level for aligning the FISH spots (now spots in the aligned images have 2-5 pixels shift). Here are my ideas: 1) use the full resolution images (but not the downsampled ones) to do the affine and deformable registration; 2) adjust the align threshold from 2.0 to 1.0 micro, or even smaller; 3) if the above methods are not applicable, do the registration with the aligned FISH channel but not with DAPI channel.

Now I used the full resolution images (but not the downsampled ones) to do the affine and deformable registration but it looks like the default images need to be scale 2? I am wondering can we update the pipeline and add the options for the high-resolution images?

I would be really appreciated it if you have suggestions. Thank you so much!

Best,
Zhenggang

[GFleishman]

Finally going through backlog issues. I didn't respond to this initially because it's essentially a feature request, and was in conflict with ongoing unpublished research I was participating in with other groups. I could not in good conscience discuss FISH spot registration openly without the approval of other stake holders in those projects. What I can say is that using the functionality already present in bigstream it is possible to register FISH spots to each other round to round - assuming the same spots are labeled of course. No new features need to be added to the package to make this work, but a good deal of experience and practice is required to learn how to utilize the existing functions to do this well.