search

JinmiaoChenLab / GraphST

GNU Affero General Public License v3.0
86 stars 9 forks source link

Adaptation for VisiumHD? #30

Closed Rafael-Silva-Oliveira closed 2 months ago

Rafael-Silva-Oliveira commented 5 months ago

Hey, with the latest release of VisiumHD, the files have become huge (barcodes going from 5-10k to over 500k in the 8 micron bins). I noticed that the GrapST package isn't very optimized in the sense that there's a lot of "copies" being made from original files which end up blowing up memory consumption (over 100 GB for a file with 400k barcodes). I was wondering if there's a goal to optimize the code to be better at managing memory with VisiumHD data?

longyahui commented 5 months ago

Hi,

Thank you for the great suggestion.

Next, we would consider optimizing the memory issue. 

Best regards,
Yahui