Run SpaceRanger for 2720 Ant (round 4)

[lcolladotor]

You can overwrite the current SpaceRanger results we have.

[lcolladotor]

We think that we need to do this because @heenadivecha identified that VistoSeg doesn't run with the Loupe alignment json info for this sample and suggested that we need to re-align the image (maybe even use a new image). It might be good to check with @madhavitippani though.

[lcolladotor]

Heena @heenadivecha explained to us what the problem is: that the fiducial frame on the top left is missing:

[madhavitippani]

While debugging, it's seen that VistoSeg when splitting the raw image missed a part of fiducial frame for capture area D1 of that sample. This happens when the center of the visium slide does not align with the center of the image, which has to be adjusted while imaging. This image when run through spaceranger provided negative coordinates for the missing fiducial frame part of the image, but MATLAB will not accept negative indices for an image, which was throwing errors when reconstructing spot grind in countSpots function.
We can calculate that offset, add it to the negative indices and make countspots function work, but I would prefer rerunning spaceranger.

[lcolladotor]

Thanks @madhavitippani for the info! So in order to resolve this, we'll need a new capture area image (to pass to SpaceRanger) and re-run SpaceRanger. That's ok!

@heenadivecha can you let us know when you have the new capture area image? Thanks!

[lcolladotor]

Heena, feel free to overwrite the older capture image since we won't use it anymore. Same with the SpaceRanger output results Abby.