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scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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sq.gr.ripley() cost too much memory #870

Open wangjiawen2013 opened 1 month ago

wangjiawen2013 commented 1 month ago

Hi, sq.gr.ripley() cost too much memory (600G) when analysing large datasets (such as xenium, up to 250,000 cells). The memory was exhausted and the analysis was interrupted.

giovp commented 4 weeks ago

hi @wangjiawen2013 , I can see the problem, unfort I don't have capacity to write a memory efficient implementation. Any help would be highly appreciated.