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Add SPIFF to walkthrough#66

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Add SPIFF to walkthrough#66
putnokiabel wants to merge 5 commits into
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@putnokiabel

@putnokiabel putnokiabel commented May 22, 2026

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Add explanation on SPIFF (see soft-matter/trackpy#799).

(I'll need to run the notebook again once the other PR is merged to actually show the results with SPIFF).

I ended up not changing the subpixel-bias section: as mentioned in soft-matter/trackpy#799 (comment), it's best to keep things simple for novices.
I added a section at the end (under "Preview of Some Advanced Features") that explains SPIFF and its usage in a bit more detail. If it's too much detail, let me know which parts I should shorten / leave out!

@putnokiabel putnokiabel marked this pull request as draft May 22, 2026 21:05
@nkeim

nkeim commented Jun 3, 2026

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Thanks @putnokiabel !! I edited this to match the house style a bit better, and to integrate it into the earlier discussion of subpixel bias. We now choose a smaller diameter for locate based on close inspection of an image. I also pointed out that SPIFF assumes that pixel locking is identical across all particles, which may not be true for everyone.

SPIFF is now used for the emsd calculation, and the results look excellent. @vivarose you might like to see the power-law fit:

Before:
Unknown

Apparently pixel-locking was suppressing the smallest displacements.

With SPIFF:
image

Please feel free to correct and revise, either with commits or just suggestions here.

Note that the execution times are often weird when I run this on my (fanless) laptop. We can try to do better before the release.

@vivarose

vivarose commented Jun 3, 2026

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Woah this is a big improvement! I don't know what pixel locking is and I want to understand fully.

@putnokiabel

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@nkeim the changes look good to me, you formulated it much more cleanly than I did 😄

I noticed a processes=1 argument went missing when adding the SPIFF argument in the parallelization section, I fixed it.
Let me know if you need anything from my end in order to merge this feature (& documentation)!

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3 participants