Xenium: cache zip store opening; vectorize cell id encoding#370
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LucaMarconato merged 7 commits intomainfrom Feb 24, 2026
Merged
Xenium: cache zip store opening; vectorize cell id encoding#370LucaMarconato merged 7 commits intomainfrom
LucaMarconato merged 7 commits intomainfrom
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #370 +/- ##
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+ Coverage 62.70% 62.86% +0.15%
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Files 27 27
Lines 3140 3156 +16
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+ Hits 1969 1984 +15
- Misses 1171 1172 +1
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I'll merge this and then also #373. I spotted a few more places where we could improve performance, I may implement them in a follow up PR. |
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After doing some profiling, I identified 2 bottlenecks:
cell_id_str_from_prefix_suffix_uint32()had some long for loops that could be removed.This PR:
cell_id_str_from_prefix_suffix_uint32()The second part is very interesting: Claude Opus 4.6 suggested a clever bit-shift trick which halves execution time (illustrated below, again with the help of Claude).
Further optimization could be explored for the string concatenation, which is now driving the runtime of the function (10% of total, see flame graph), and is among the top 3 drivers of runtime.
Flame graph:

Explanation of the bit shift trick:
